Starting phenix.real_space_refine on Thu Sep 26 17:26:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/09_2024/5bk4_9400.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/09_2024/5bk4_9400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/09_2024/5bk4_9400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/09_2024/5bk4_9400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/09_2024/5bk4_9400.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5bk4_9400/09_2024/5bk4_9400.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 136 5.49 5 S 268 5.16 5 C 38860 2.51 5 N 10966 2.21 5 O 12252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 62482 Number of models: 1 Model: "" Number of chains: 22 Chain: "2" Number of atoms: 4714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4714 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 14, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 565} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "3" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4734 Classifications: {'peptide': 604} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 568} Chain breaks: 3 Chain: "4" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5127 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 10, 'PTRANS': 23, 'TRANS': 612} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 5165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5165 Classifications: {'peptide': 661} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 616} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4731 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 25, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 567} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "7" Number of atoms: 5432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5432 Classifications: {'peptide': 689} Link IDs: {'CIS': 12, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 646} Chain breaks: 3 Chain: "A" Number of atoms: 4714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4714 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 14, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 565} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4734 Classifications: {'peptide': 604} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 568} Chain breaks: 3 Chain: "C" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5127 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 10, 'PTRANS': 23, 'TRANS': 612} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 5165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5165 Classifications: {'peptide': 661} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 616} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4731 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 25, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 567} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "F" Number of atoms: 5432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5432 Classifications: {'peptide': 689} Link IDs: {'CIS': 12, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 646} Chain breaks: 3 Chain: "S" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "O" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1230 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "2" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.61, per 1000 atoms: 0.46 Number of scatterers: 62482 At special positions: 0 Unit cell: (163.2, 223.04, 154.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 268 16.00 P 136 15.00 O 12252 8.00 N 10966 7.00 C 38860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS 5 183 " - pdb=" SG CYS 5 211 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 183 " - pdb=" SG CYS 5 236 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 211 " distance=2.02 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 236 " distance=2.02 Simple disulfide: pdb=" SG CYS 5 211 " - pdb=" SG CYS 5 236 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 265 " - pdb=" SG CYS 7 289 " distance=2.02 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " distance=2.04 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 211 " distance=2.04 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 236 " distance=2.04 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 211 " distance=2.02 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 236 " distance=2.02 Simple disulfide: pdb=" SG CYS D 211 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 265 " - pdb=" SG CYS F 289 " distance=2.02 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 522 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.69 Conformation dependent library (CDL) restraints added in 6.0 seconds 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14508 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 88 sheets defined 38.4% alpha, 10.6% beta 57 base pairs and 113 stacking pairs defined. Time for finding SS restraints: 16.39 Creating SS restraints... Processing helix chain '2' and resid 203 through 216 removed outlier: 3.650A pdb=" N ILE 2 207 " --> pdb=" O VAL 2 203 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG 2 209 " --> pdb=" O ARG 2 205 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU 2 216 " --> pdb=" O LYS 2 212 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 232 Processing helix chain '2' and resid 245 through 253 removed outlier: 4.208A pdb=" N LEU 2 249 " --> pdb=" O ASN 2 245 " (cutoff:3.500A) Processing helix chain '2' and resid 253 through 262 removed outlier: 3.773A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 4.093A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 290 removed outlier: 4.464A pdb=" N ILE 2 289 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS 2 290 " --> pdb=" O TYR 2 286 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 285 through 290' Processing helix chain '2' and resid 310 through 314 removed outlier: 3.511A pdb=" N ASN 2 313 " --> pdb=" O ARG 2 310 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 2 314 " --> pdb=" O GLU 2 311 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 310 through 314' Processing helix chain '2' and resid 411 through 415 removed outlier: 3.894A pdb=" N VAL 2 415 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 483 Processing helix chain '2' and resid 483 through 489 removed outlier: 4.489A pdb=" N ILE 2 487 " --> pdb=" O GLU 2 483 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER 2 488 " --> pdb=" O PHE 2 484 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG 2 489 " --> pdb=" O ARG 2 485 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 483 through 489' Processing helix chain '2' and resid 492 through 500 removed outlier: 3.543A pdb=" N LYS 2 496 " --> pdb=" O GLY 2 492 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 removed outlier: 3.791A pdb=" N GLY 2 521 " --> pdb=" O CYS 2 517 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 560 removed outlier: 3.587A pdb=" N LYS 2 558 " --> pdb=" O LYS 2 554 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 608 through 612 removed outlier: 3.598A pdb=" N LYS 2 611 " --> pdb=" O GLU 2 608 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET 2 612 " --> pdb=" O PHE 2 609 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 608 through 612' Processing helix chain '2' and resid 613 through 626 removed outlier: 3.693A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN 2 626 " --> pdb=" O GLU 2 622 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 Processing helix chain '2' and resid 688 through 704 removed outlier: 3.659A pdb=" N PHE 2 698 " --> pdb=" O ARG 2 694 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 773 removed outlier: 3.802A pdb=" N LEU 2 763 " --> pdb=" O PRO 2 759 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS 2 773 " --> pdb=" O TYR 2 769 " (cutoff:3.500A) Processing helix chain '2' and resid 783 through 797 removed outlier: 4.270A pdb=" N SER 2 787 " --> pdb=" O MET 2 783 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG 2 788 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU 2 796 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 823 removed outlier: 4.193A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 847 removed outlier: 3.965A pdb=" N LEU 2 834 " --> pdb=" O SER 2 830 " (cutoff:3.500A) Processing helix chain '2' and resid 850 through 852 No H-bonds generated for 'chain '2' and resid 850 through 852' Processing helix chain '2' and resid 853 through 858 removed outlier: 3.717A pdb=" N ARG 2 858 " --> pdb=" O ARG 2 854 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 35 Processing helix chain '3' and resid 36 through 59 removed outlier: 3.994A pdb=" N ASP 3 40 " --> pdb=" O THR 3 36 " (cutoff:3.500A) Processing helix chain '3' and resid 101 through 105 removed outlier: 3.583A pdb=" N ARG 3 104 " --> pdb=" O ASP 3 101 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 115 Processing helix chain '3' and resid 121 through 137 removed outlier: 3.864A pdb=" N ALA 3 125 " --> pdb=" O PHE 3 121 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP 3 137 " --> pdb=" O ALA 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 279 through 283 removed outlier: 3.714A pdb=" N LEU 3 282 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL 3 283 " --> pdb=" O ASP 3 280 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 279 through 283' Processing helix chain '3' and resid 343 through 354 Processing helix chain '3' and resid 358 through 365 removed outlier: 3.848A pdb=" N GLN 3 365 " --> pdb=" O ASP 3 361 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 removed outlier: 3.713A pdb=" N LYS 3 378 " --> pdb=" O HIS 3 374 " (cutoff:3.500A) Processing helix chain '3' and resid 414 through 426 removed outlier: 4.157A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG 3 420 " --> pdb=" O SER 3 416 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE 3 421 " --> pdb=" O GLN 3 417 " (cutoff:3.500A) Processing helix chain '3' and resid 474 through 478 removed outlier: 3.685A pdb=" N MET 3 478 " --> pdb=" O PHE 3 475 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 491 removed outlier: 3.941A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 537 through 543 removed outlier: 3.841A pdb=" N PHE 3 543 " --> pdb=" O LEU 3 539 " (cutoff:3.500A) Processing helix chain '3' and resid 555 through 569 removed outlier: 3.784A pdb=" N HIS 3 564 " --> pdb=" O SER 3 560 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS 3 569 " --> pdb=" O VAL 3 565 " (cutoff:3.500A) Processing helix chain '3' and resid 652 through 666 removed outlier: 4.445A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR 3 662 " --> pdb=" O LYS 3 658 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG 3 666 " --> pdb=" O TYR 3 662 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 674 No H-bonds generated for 'chain '3' and resid 672 through 674' Processing helix chain '3' and resid 675 through 694 removed outlier: 3.821A pdb=" N ILE 3 679 " --> pdb=" O ALA 3 675 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR 3 692 " --> pdb=" O ASN 3 688 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 716 removed outlier: 4.164A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG 3 716 " --> pdb=" O HIS 3 712 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 removed outlier: 4.034A pdb=" N ALA 3 726 " --> pdb=" O ASN 3 722 " (cutoff:3.500A) Processing helix chain '4' and resid 186 through 198 Processing helix chain '4' and resid 203 through 210 Processing helix chain '4' and resid 224 through 236 removed outlier: 4.201A pdb=" N LYS 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU 4 236 " --> pdb=" O GLU 4 232 " (cutoff:3.500A) Processing helix chain '4' and resid 245 through 251 removed outlier: 3.733A pdb=" N TYR 4 251 " --> pdb=" O ASN 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 255 through 264 removed outlier: 4.241A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN 4 263 " --> pdb=" O HIS 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 285 removed outlier: 3.777A pdb=" N VAL 4 268 " --> pdb=" O TYR 4 264 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL 4 285 " --> pdb=" O VAL 4 281 " (cutoff:3.500A) Processing helix chain '4' and resid 292 through 299 removed outlier: 4.325A pdb=" N ILE 4 296 " --> pdb=" O ASP 4 292 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU 4 297 " --> pdb=" O LEU 4 293 " (cutoff:3.500A) Processing helix chain '4' and resid 420 through 424 removed outlier: 3.513A pdb=" N VAL 4 424 " --> pdb=" O ASP 4 421 " (cutoff:3.500A) Processing helix chain '4' and resid 482 through 488 Processing helix chain '4' and resid 503 through 513 removed outlier: 3.998A pdb=" N ALA 4 507 " --> pdb=" O ASP 4 503 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS 4 508 " --> pdb=" O GLN 4 504 " (cutoff:3.500A) Processing helix chain '4' and resid 514 through 516 No H-bonds generated for 'chain '4' and resid 514 through 516' Processing helix chain '4' and resid 517 through 525 removed outlier: 4.286A pdb=" N ALA 4 523 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 544 removed outlier: 3.627A pdb=" N LEU 4 544 " --> pdb=" O ILE 4 540 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 removed outlier: 4.013A pdb=" N ILE 4 577 " --> pdb=" O SER 4 573 " (cutoff:3.500A) Processing helix chain '4' and resid 598 through 602 removed outlier: 4.145A pdb=" N LEU 4 601 " --> pdb=" O ALA 4 598 " (cutoff:3.500A) Processing helix chain '4' and resid 633 through 637 removed outlier: 4.118A pdb=" N MET 4 637 " --> pdb=" O PHE 4 634 " (cutoff:3.500A) Processing helix chain '4' and resid 644 through 649 removed outlier: 3.576A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 695 through 702 removed outlier: 3.751A pdb=" N PHE 4 702 " --> pdb=" O LEU 4 698 " (cutoff:3.500A) Processing helix chain '4' and resid 714 through 729 removed outlier: 4.091A pdb=" N ARG 4 718 " --> pdb=" O GLU 4 714 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) Processing helix chain '4' and resid 730 through 732 No H-bonds generated for 'chain '4' and resid 730 through 732' Processing helix chain '4' and resid 745 through 757 removed outlier: 4.189A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS 4 757 " --> pdb=" O TYR 4 753 " (cutoff:3.500A) Processing helix chain '4' and resid 763 through 765 No H-bonds generated for 'chain '4' and resid 763 through 765' Processing helix chain '4' and resid 766 through 779 Processing helix chain '4' and resid 794 through 811 removed outlier: 3.884A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET 4 811 " --> pdb=" O ALA 4 807 " (cutoff:3.500A) Processing helix chain '4' and resid 821 through 835 removed outlier: 3.687A pdb=" N ALA 4 825 " --> pdb=" O ASP 4 821 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 36 removed outlier: 3.641A pdb=" N PHE 5 31 " --> pdb=" O ILE 5 27 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU 5 36 " --> pdb=" O LYS 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 56 removed outlier: 3.509A pdb=" N GLN 5 49 " --> pdb=" O ILE 5 45 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU 5 55 " --> pdb=" O ARG 5 51 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 73 through 82 removed outlier: 3.780A pdb=" N LYS 5 77 " --> pdb=" O GLU 5 73 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU 5 82 " --> pdb=" O LYS 5 78 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 85 No H-bonds generated for 'chain '5' and resid 83 through 85' Processing helix chain '5' and resid 86 through 108 removed outlier: 3.977A pdb=" N VAL 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 152 through 156 removed outlier: 3.659A pdb=" N VAL 5 156 " --> pdb=" O SER 5 153 " (cutoff:3.500A) Processing helix chain '5' and resid 219 through 225 Processing helix chain '5' and resid 351 through 361 Processing helix chain '5' and resid 365 through 371 Processing helix chain '5' and resid 381 through 388 Processing helix chain '5' and resid 421 through 433 Processing helix chain '5' and resid 489 through 494 removed outlier: 3.873A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) Processing helix chain '5' and resid 527 through 531 removed outlier: 3.638A pdb=" N TYR 5 530 " --> pdb=" O TYR 5 527 " (cutoff:3.500A) Processing helix chain '5' and resid 545 through 550 removed outlier: 3.513A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) Processing helix chain '5' and resid 561 through 577 removed outlier: 3.748A pdb=" N THR 5 577 " --> pdb=" O ILE 5 573 " (cutoff:3.500A) Processing helix chain '5' and resid 579 through 590 Processing helix chain '5' and resid 596 through 609 removed outlier: 3.943A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 640 removed outlier: 4.374A pdb=" N THR 5 628 " --> pdb=" O SER 5 624 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 668 removed outlier: 3.927A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR 5 660 " --> pdb=" O ILE 5 656 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU 5 661 " --> pdb=" O ILE 5 657 " (cutoff:3.500A) Processing helix chain '5' and resid 674 through 693 removed outlier: 4.711A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER 5 693 " --> pdb=" O MET 5 689 " (cutoff:3.500A) Processing helix chain '6' and resid 104 through 121 removed outlier: 3.604A pdb=" N ASP 6 121 " --> pdb=" O GLN 6 117 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 147 removed outlier: 3.764A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 162 removed outlier: 3.589A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 166 through 171 removed outlier: 3.672A pdb=" N SER 6 171 " --> pdb=" O ALA 6 167 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 176 No H-bonds generated for 'chain '6' and resid 174 through 176' Processing helix chain '6' and resid 177 through 193 removed outlier: 3.920A pdb=" N LEU 6 181 " --> pdb=" O PHE 6 177 " (cutoff:3.500A) Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 512 through 519 Processing helix chain '6' and resid 524 through 532 Processing helix chain '6' and resid 541 through 551 Processing helix chain '6' and resid 581 through 592 removed outlier: 3.935A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 645 through 658 Processing helix chain '6' and resid 694 through 699 removed outlier: 3.740A pdb=" N LEU 6 699 " --> pdb=" O ARG 6 696 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 735 Processing helix chain '6' and resid 747 through 759 removed outlier: 3.960A pdb=" N LEU 6 751 " --> pdb=" O SER 6 747 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG 6 752 " --> pdb=" O ALA 6 748 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS 6 756 " --> pdb=" O ARG 6 752 " (cutoff:3.500A) Processing helix chain '6' and resid 769 through 784 removed outlier: 4.319A pdb=" N ASP 6 783 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 814 removed outlier: 3.941A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE 6 804 " --> pdb=" O LEU 6 800 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG 6 805 " --> pdb=" O GLU 6 801 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 840 removed outlier: 3.916A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL 6 838 " --> pdb=" O SER 6 834 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL 6 840 " --> pdb=" O ILE 6 836 " (cutoff:3.500A) Processing helix chain '7' and resid 15 through 27 removed outlier: 3.817A pdb=" N ASN 7 19 " --> pdb=" O ASN 7 15 " (cutoff:3.500A) Processing helix chain '7' and resid 62 through 72 removed outlier: 3.523A pdb=" N MET 7 66 " --> pdb=" O LYS 7 62 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 96 Processing helix chain '7' and resid 102 through 110 removed outlier: 3.759A pdb=" N ASN 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 122 removed outlier: 4.621A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 138 through 161 removed outlier: 3.907A pdb=" N ARG 7 157 " --> pdb=" O MET 7 153 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR 7 158 " --> pdb=" O LEU 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 162 through 164 No H-bonds generated for 'chain '7' and resid 162 through 164' Processing helix chain '7' and resid 178 through 186 Processing helix chain '7' and resid 208 through 216 removed outlier: 3.815A pdb=" N ALA 7 212 " --> pdb=" O SER 7 208 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 363 through 367 removed outlier: 3.583A pdb=" N LYS 7 367 " --> pdb=" O LYS 7 364 " (cutoff:3.500A) Processing helix chain '7' and resid 397 through 406 removed outlier: 4.326A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 418 removed outlier: 3.546A pdb=" N ARG 7 413 " --> pdb=" O ASP 7 409 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 438 removed outlier: 3.564A pdb=" N LYS 7 429 " --> pdb=" O ASN 7 425 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) Processing helix chain '7' and resid 466 through 477 Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 525 through 529 removed outlier: 3.625A pdb=" N MET 7 529 " --> pdb=" O PHE 7 526 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 542 removed outlier: 3.578A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 587 through 594 Processing helix chain '7' and resid 607 through 622 removed outlier: 4.331A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 646 removed outlier: 3.529A pdb=" N LYS 7 646 " --> pdb=" O ILE 7 642 " (cutoff:3.500A) Processing helix chain '7' and resid 654 through 672 removed outlier: 3.800A pdb=" N LYS 7 672 " --> pdb=" O ARG 7 668 " (cutoff:3.500A) Processing helix chain '7' and resid 686 through 700 Processing helix chain '7' and resid 701 through 704 Processing helix chain '7' and resid 709 through 724 removed outlier: 3.695A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.651A pdb=" N ILE A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 245 through 253 removed outlier: 4.208A pdb=" N LEU A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.774A pdb=" N ALA A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 283 removed outlier: 4.094A pdb=" N MET A 267 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.464A pdb=" N ILE A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 290' Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.511A pdb=" N ASN A 313 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 314 " --> pdb=" O GLU A 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 314' Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.895A pdb=" N VAL A 415 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 483 through 489 removed outlier: 4.489A pdb=" N ILE A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 489' Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.543A pdb=" N LYS A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 removed outlier: 3.791A pdb=" N GLY A 521 " --> pdb=" O CYS A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.587A pdb=" N LYS A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 608 through 612 removed outlier: 3.598A pdb=" N LYS A 611 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 612 " --> pdb=" O PHE A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 612' Processing helix chain 'A' and resid 613 through 626 removed outlier: 3.693A pdb=" N SER A 619 " --> pdb=" O GLN A 615 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 688 through 704 removed outlier: 3.659A pdb=" N PHE A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 773 removed outlier: 3.802A pdb=" N LEU A 763 " --> pdb=" O PRO A 759 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 768 " --> pdb=" O MET A 764 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 773 " --> pdb=" O TYR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 797 removed outlier: 4.270A pdb=" N SER A 787 " --> pdb=" O MET A 783 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 788 " --> pdb=" O ASP A 784 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 823 removed outlier: 4.193A pdb=" N ILE A 813 " --> pdb=" O HIS A 809 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 847 removed outlier: 3.965A pdb=" N LEU A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.718A pdb=" N ARG A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 35 Processing helix chain 'B' and resid 36 through 59 removed outlier: 3.995A pdb=" N ASP B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.583A pdb=" N ARG B 104 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 121 through 137 removed outlier: 3.864A pdb=" N ALA B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.712A pdb=" N LEU B 282 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 283 " --> pdb=" O ASP B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 283' Processing helix chain 'B' and resid 343 through 354 Processing helix chain 'B' and resid 358 through 365 removed outlier: 3.848A pdb=" N GLN B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 387 removed outlier: 3.713A pdb=" N LYS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 removed outlier: 4.156A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.685A pdb=" N MET B 478 " --> pdb=" O PHE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.942A pdb=" N ALA B 485 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU B 491 " --> pdb=" O HIS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.842A pdb=" N PHE B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 569 removed outlier: 3.784A pdb=" N HIS B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 666 removed outlier: 4.445A pdb=" N LYS B 658 " --> pdb=" O PRO B 654 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 662 " --> pdb=" O LYS B 658 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 666 " --> pdb=" O TYR B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 674 No H-bonds generated for 'chain 'B' and resid 672 through 674' Processing helix chain 'B' and resid 675 through 694 removed outlier: 3.821A pdb=" N ILE B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR B 692 " --> pdb=" O ASN B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 716 removed outlier: 4.164A pdb=" N LEU B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG B 716 " --> pdb=" O HIS B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 738 removed outlier: 4.034A pdb=" N ALA B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 198 Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 224 through 236 removed outlier: 4.200A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 removed outlier: 3.734A pdb=" N TYR C 251 " --> pdb=" O ASN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 removed outlier: 4.241A pdb=" N HIS C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 285 removed outlier: 3.777A pdb=" N VAL C 268 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 4.325A pdb=" N ILE C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 removed outlier: 3.512A pdb=" N VAL C 424 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 488 Processing helix chain 'C' and resid 503 through 513 removed outlier: 3.998A pdb=" N ALA C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 508 " --> pdb=" O GLN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 516 No H-bonds generated for 'chain 'C' and resid 514 through 516' Processing helix chain 'C' and resid 517 through 525 removed outlier: 4.285A pdb=" N ALA C 523 " --> pdb=" O TYR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 544 removed outlier: 3.628A pdb=" N LEU C 544 " --> pdb=" O ILE C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 585 removed outlier: 4.014A pdb=" N ILE C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 removed outlier: 4.145A pdb=" N LEU C 601 " --> pdb=" O ALA C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 637 removed outlier: 4.118A pdb=" N MET C 637 " --> pdb=" O PHE C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 649 removed outlier: 3.576A pdb=" N VAL C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 702 removed outlier: 3.751A pdb=" N PHE C 702 " --> pdb=" O LEU C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 729 removed outlier: 4.092A pdb=" N ARG C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU C 719 " --> pdb=" O LYS C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 732 No H-bonds generated for 'chain 'C' and resid 730 through 732' Processing helix chain 'C' and resid 745 through 757 removed outlier: 4.187A pdb=" N MET C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS C 757 " --> pdb=" O TYR C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'C' and resid 766 through 779 Processing helix chain 'C' and resid 794 through 811 removed outlier: 3.884A pdb=" N LEU C 798 " --> pdb=" O THR C 794 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET C 811 " --> pdb=" O ALA C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 835 removed outlier: 3.689A pdb=" N ALA C 825 " --> pdb=" O ASP C 821 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE C 829 " --> pdb=" O ALA C 825 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA C 832 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 36 removed outlier: 3.640A pdb=" N PHE D 31 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 56 removed outlier: 3.507A pdb=" N GLN D 49 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 56 " --> pdb=" O ASN D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.781A pdb=" N LYS D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 86 through 108 removed outlier: 3.978A pdb=" N VAL D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 156 removed outlier: 3.659A pdb=" N VAL D 156 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 225 Processing helix chain 'D' and resid 351 through 361 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 381 through 388 Processing helix chain 'D' and resid 421 through 433 Processing helix chain 'D' and resid 489 through 494 removed outlier: 3.873A pdb=" N ILE D 493 " --> pdb=" O ASP D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 531 removed outlier: 3.638A pdb=" N TYR D 530 " --> pdb=" O TYR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 550 removed outlier: 3.512A pdb=" N PHE D 550 " --> pdb=" O ILE D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 577 removed outlier: 3.747A pdb=" N THR D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 596 through 609 removed outlier: 3.943A pdb=" N ARG D 601 " --> pdb=" O GLU D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 640 removed outlier: 4.374A pdb=" N THR D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 668 removed outlier: 3.926A pdb=" N LEU D 653 " --> pdb=" O THR D 649 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR D 660 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 661 " --> pdb=" O ILE D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 693 removed outlier: 4.711A pdb=" N ALA D 680 " --> pdb=" O HIS D 676 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER D 693 " --> pdb=" O MET D 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 121 removed outlier: 3.605A pdb=" N ASP E 121 " --> pdb=" O GLN E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.765A pdb=" N TYR E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 162 removed outlier: 3.589A pdb=" N ARG E 161 " --> pdb=" O HIS E 157 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.672A pdb=" N SER E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 177 through 193 removed outlier: 3.920A pdb=" N LEU E 181 " --> pdb=" O PHE E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 512 through 519 Processing helix chain 'E' and resid 524 through 532 Processing helix chain 'E' and resid 541 through 551 Processing helix chain 'E' and resid 581 through 592 removed outlier: 3.934A pdb=" N LEU E 585 " --> pdb=" O LYS E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 658 Processing helix chain 'E' and resid 694 through 699 removed outlier: 3.740A pdb=" N LEU E 699 " --> pdb=" O ARG E 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 735 Processing helix chain 'E' and resid 747 through 759 removed outlier: 3.960A pdb=" N LEU E 751 " --> pdb=" O SER E 747 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG E 752 " --> pdb=" O ALA E 748 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 756 " --> pdb=" O ARG E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 769 through 784 removed outlier: 4.319A pdb=" N ASP E 783 " --> pdb=" O GLU E 779 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP E 784 " --> pdb=" O LEU E 780 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 814 removed outlier: 3.941A pdb=" N LEU E 800 " --> pdb=" O THR E 796 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE E 804 " --> pdb=" O LEU E 800 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG E 805 " --> pdb=" O GLU E 801 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 840 removed outlier: 3.916A pdb=" N ILE E 824 " --> pdb=" O THR E 820 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL E 838 " --> pdb=" O SER E 834 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL E 840 " --> pdb=" O ILE E 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 27 removed outlier: 3.817A pdb=" N ASN F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 3.523A pdb=" N MET F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'F' and resid 102 through 110 removed outlier: 3.759A pdb=" N ASN F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 122 removed outlier: 4.622A pdb=" N GLU F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 161 removed outlier: 3.906A pdb=" N ARG F 157 " --> pdb=" O MET F 153 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 178 through 186 Processing helix chain 'F' and resid 208 through 216 removed outlier: 3.815A pdb=" N ALA F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR F 215 " --> pdb=" O CYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 363 through 367 removed outlier: 3.583A pdb=" N LYS F 367 " --> pdb=" O LYS F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 406 removed outlier: 4.326A pdb=" N GLU F 403 " --> pdb=" O GLU F 399 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU F 404 " --> pdb=" O ARG F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 418 removed outlier: 3.546A pdb=" N ARG F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 438 removed outlier: 3.565A pdb=" N LYS F 429 " --> pdb=" O ASN F 425 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU F 434 " --> pdb=" O LYS F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 477 Processing helix chain 'F' and resid 511 through 516 Processing helix chain 'F' and resid 525 through 529 removed outlier: 3.624A pdb=" N MET F 529 " --> pdb=" O PHE F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 542 removed outlier: 3.577A pdb=" N GLU F 542 " --> pdb=" O HIS F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 594 Processing helix chain 'F' and resid 607 through 622 removed outlier: 4.330A pdb=" N LYS F 611 " --> pdb=" O ASP F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 646 removed outlier: 3.530A pdb=" N LYS F 646 " --> pdb=" O ILE F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 672 removed outlier: 3.800A pdb=" N LYS F 672 " --> pdb=" O ARG F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 700 Processing helix chain 'F' and resid 701 through 704 Processing helix chain 'F' and resid 709 through 724 removed outlier: 3.694A pdb=" N VAL F 713 " --> pdb=" O ASP F 709 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS F 724 " --> pdb=" O VAL F 720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 242 removed outlier: 3.541A pdb=" N LEU 2 242 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 331 through 334 removed outlier: 7.291A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR 2 325 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY 2 322 " --> pdb=" O VAL 2 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 331 through 334 removed outlier: 3.803A pdb=" N GLN 2 386 " --> pdb=" O LEU 2 410 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE 2 450 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 539 through 542 Processing sheet with id=AA5, first strand: chain '2' and resid 563 through 565 removed outlier: 7.025A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '2' and resid 579 through 581 removed outlier: 3.714A pdb=" N GLU 2 592 " --> pdb=" O SER 2 579 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 628 through 631 Processing sheet with id=AA8, first strand: chain '3' and resid 327 through 328 Processing sheet with id=AA9, first strand: chain '3' and resid 193 through 196 Processing sheet with id=AB1, first strand: chain '3' and resid 198 through 199 removed outlier: 3.789A pdb=" N ARG 3 212 " --> pdb=" O SER 3 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 201 through 203 Processing sheet with id=AB3, first strand: chain '3' and resid 429 through 433 removed outlier: 6.645A pdb=" N ILE 3 430 " --> pdb=" O CYS 3 471 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASP 3 473 " --> pdb=" O ILE 3 430 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA 3 515 " --> pdb=" O ILE 3 472 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL 3 408 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 494 through 497 removed outlier: 3.775A pdb=" N VAL 3 495 " --> pdb=" O LEU 3 506 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE 3 497 " --> pdb=" O THR 3 504 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 241 through 243 removed outlier: 7.092A pdb=" N LEU 4 241 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 325 through 328 removed outlier: 3.503A pdb=" N GLY 4 437 " --> pdb=" O ILE 4 326 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL 4 435 " --> pdb=" O LEU 4 328 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS 4 458 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 325 through 328 removed outlier: 3.503A pdb=" N GLY 4 437 " --> pdb=" O ILE 4 326 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL 4 435 " --> pdb=" O LEU 4 328 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS 4 465 " --> pdb=" O THR 4 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 331 through 335 removed outlier: 7.145A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 347 through 348 Processing sheet with id=AC1, first strand: chain '4' and resid 589 through 590 removed outlier: 6.747A pdb=" N VAL 4 589 " --> pdb=" O CYS 4 630 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE 4 564 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ALA 4 675 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU 4 566 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 606 through 608 removed outlier: 3.826A pdb=" N GLN 4 613 " --> pdb=" O ASP 4 608 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '4' and resid 654 through 656 removed outlier: 4.346A pdb=" N ILE 4 656 " --> pdb=" O THR 4 663 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR 4 663 " --> pdb=" O ILE 4 656 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '5' and resid 61 through 64 removed outlier: 6.294A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain '5' and resid 159 through 161 Processing sheet with id=AC6, first strand: chain '5' and resid 273 through 275 removed outlier: 3.817A pdb=" N LEU 5 258 " --> pdb=" O LEU 5 274 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY 5 164 " --> pdb=" O VAL 5 292 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL 5 292 " --> pdb=" O GLY 5 164 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 192 through 193 removed outlier: 6.969A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU 5 179 " --> pdb=" O SER 5 247 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N SER 5 247 " --> pdb=" O LEU 5 179 " (cutoff:3.500A) removed outlier: 10.497A pdb=" N ILE 5 181 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N HIS 5 245 " --> pdb=" O ILE 5 181 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N CYS 5 183 " --> pdb=" O ILE 5 243 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N ILE 5 243 " --> pdb=" O CYS 5 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 412 through 416 removed outlier: 6.336A pdb=" N LEU 5 413 " --> pdb=" O PHE 5 554 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL 5 556 " --> pdb=" O LEU 5 413 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU 5 415 " --> pdb=" O VAL 5 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '5' and resid 436 through 439 removed outlier: 6.618A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP 5 480 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR 5 439 " --> pdb=" O ASP 5 480 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '5' and resid 452 through 456 removed outlier: 7.038A pdb=" N SER 5 452 " --> pdb=" O GLU 5 465 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN 5 454 " --> pdb=" O TYR 5 463 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR 5 463 " --> pdb=" O GLN 5 454 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 151 through 152 removed outlier: 7.013A pdb=" N ILE 6 151 " --> pdb=" O SER 6 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain '6' and resid 273 through 274 removed outlier: 3.940A pdb=" N SER 6 291 " --> pdb=" O HIS 6 274 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 273 through 274 removed outlier: 3.940A pdb=" N SER 6 291 " --> pdb=" O HIS 6 274 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY 6 292 " --> pdb=" O CYS 6 395 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS 6 395 " --> pdb=" O GLY 6 292 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '6' and resid 301 through 303 removed outlier: 3.523A pdb=" N ARG 6 301 " --> pdb=" O TRP 6 356 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU 6 354 " --> pdb=" O GLU 6 303 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE 6 380 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '6' and resid 307 through 308 removed outlier: 4.046A pdb=" N ALA 6 307 " --> pdb=" O ASN 6 320 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 403 through 406 removed outlier: 4.184A pdb=" N THR 6 449 " --> pdb=" O ASP 6 406 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '6' and resid 595 through 598 removed outlier: 6.530A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU 6 679 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY 6 575 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ILE 6 715 " --> pdb=" O CYS 6 572 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL 6 574 " --> pdb=" O ILE 6 715 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '6' and resid 660 through 664 Processing sheet with id=AE1, first strand: chain '7' and resid 79 through 81 removed outlier: 3.562A pdb=" N LYS 7 205 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 238 through 240 Processing sheet with id=AE3, first strand: chain '7' and resid 244 through 246 Processing sheet with id=AE4, first strand: chain '7' and resid 254 through 261 removed outlier: 6.817A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE 7 258 " --> pdb=" O ALA 7 304 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ALA 7 304 " --> pdb=" O ILE 7 258 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N TYR 7 260 " --> pdb=" O THR 7 302 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N THR 7 302 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '7' and resid 442 through 443 removed outlier: 3.748A pdb=" N LYS 7 442 " --> pdb=" O ILE 7 450 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '7' and resid 480 through 483 removed outlier: 6.232A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '7' and resid 496 through 498 removed outlier: 3.695A pdb=" N MET 7 498 " --> pdb=" O ILE 7 507 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE 7 507 " --> pdb=" O MET 7 498 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '7' and resid 546 through 547 removed outlier: 3.544A pdb=" N ILE 7 546 " --> pdb=" O LEU 7 557 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 241 through 242 removed outlier: 3.540A pdb=" N LEU A 242 " --> pdb=" O HIS A 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'A' and resid 331 through 334 removed outlier: 7.292A pdb=" N ARG A 387 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG A 327 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N THR A 389 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 325 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 322 " --> pdb=" O VAL A 424 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 331 through 334 removed outlier: 3.802A pdb=" N GLN A 386 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ILE A 451 " --> pdb=" O HIS A 405 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU A 407 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 450 " --> pdb=" O LYS A 431 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 539 through 542 Processing sheet with id=AF4, first strand: chain 'A' and resid 563 through 565 removed outlier: 7.026A pdb=" N VAL A 564 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N CYS A 604 " --> pdb=" O ILE A 647 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'A' and resid 579 through 581 removed outlier: 3.714A pdb=" N GLU A 592 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 628 through 631 Processing sheet with id=AF7, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AF8, first strand: chain 'B' and resid 193 through 196 Processing sheet with id=AF9, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.790A pdb=" N ARG B 212 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AG2, first strand: chain 'B' and resid 429 through 433 removed outlier: 6.646A pdb=" N ILE B 430 " --> pdb=" O CYS B 471 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASP B 473 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR B 432 " --> pdb=" O ASP B 473 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 515 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 409 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 406 " --> pdb=" O PHE B 547 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL B 549 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 408 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 494 through 497 removed outlier: 3.775A pdb=" N VAL B 495 " --> pdb=" O LEU B 506 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 497 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 241 through 243 removed outlier: 7.092A pdb=" N LEU C 241 " --> pdb=" O ARG C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.504A pdb=" N GLY C 437 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 435 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS C 458 " --> pdb=" O ILE C 442 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.504A pdb=" N GLY C 437 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 435 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS C 465 " --> pdb=" O THR C 436 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 331 through 335 removed outlier: 7.145A pdb=" N LYS C 398 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 347 through 348 Processing sheet with id=AG9, first strand: chain 'C' and resid 589 through 590 removed outlier: 6.748A pdb=" N VAL C 589 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 564 " --> pdb=" O ALA C 673 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ALA C 675 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU C 566 " --> pdb=" O ALA C 675 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 606 through 608 removed outlier: 3.826A pdb=" N GLN C 613 " --> pdb=" O ASP C 608 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.346A pdb=" N ILE C 656 " --> pdb=" O THR C 663 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 663 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 61 through 64 removed outlier: 6.294A pdb=" N LEU D 61 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASN D 140 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 63 " --> pdb=" O ASN D 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AH5, first strand: chain 'D' and resid 273 through 275 removed outlier: 3.817A pdb=" N LEU D 258 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY D 164 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 292 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 192 through 193 removed outlier: 6.968A pdb=" N LYS D 249 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU D 179 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N SER D 247 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 10.497A pdb=" N ILE D 181 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N HIS D 245 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N CYS D 183 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N ILE D 243 " --> pdb=" O CYS D 183 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 412 through 416 removed outlier: 6.336A pdb=" N LEU D 413 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL D 556 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU D 415 " --> pdb=" O VAL D 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'D' and resid 436 through 439 removed outlier: 6.619A pdb=" N VAL D 437 " --> pdb=" O CYS D 478 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASP D 480 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR D 439 " --> pdb=" O ASP D 480 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL D 477 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA D 522 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE D 479 " --> pdb=" O ALA D 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'D' and resid 452 through 456 removed outlier: 7.037A pdb=" N SER D 452 " --> pdb=" O GLU D 465 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN D 454 " --> pdb=" O TYR D 463 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR D 463 " --> pdb=" O GLN D 454 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 151 through 152 removed outlier: 7.013A pdb=" N ILE E 151 " --> pdb=" O SER E 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'E' and resid 273 through 274 removed outlier: 3.940A pdb=" N SER E 291 " --> pdb=" O HIS E 274 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 273 through 274 removed outlier: 3.940A pdb=" N SER E 291 " --> pdb=" O HIS E 274 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY E 292 " --> pdb=" O CYS E 395 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS E 395 " --> pdb=" O GLY E 292 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 301 through 303 removed outlier: 3.524A pdb=" N ARG E 301 " --> pdb=" O TRP E 356 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 354 " --> pdb=" O GLU E 303 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE E 380 " --> pdb=" O ALA E 456 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 307 through 308 removed outlier: 4.045A pdb=" N ALA E 307 " --> pdb=" O ASN E 320 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 403 through 406 removed outlier: 4.184A pdb=" N THR E 449 " --> pdb=" O ASP E 406 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 595 through 598 removed outlier: 6.530A pdb=" N VAL E 596 " --> pdb=" O CYS E 637 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASP E 639 " --> pdb=" O VAL E 596 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR E 598 " --> pdb=" O ASP E 639 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 679 " --> pdb=" O CYS E 636 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY E 575 " --> pdb=" O ALA E 682 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ILE E 715 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL E 574 " --> pdb=" O ILE E 715 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 660 through 664 Processing sheet with id=AI9, first strand: chain 'F' and resid 79 through 81 removed outlier: 3.561A pdb=" N LYS F 205 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 238 through 240 Processing sheet with id=AJ2, first strand: chain 'F' and resid 244 through 246 Processing sheet with id=AJ3, first strand: chain 'F' and resid 254 through 261 removed outlier: 6.817A pdb=" N LYS F 306 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 258 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ALA F 304 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N TYR F 260 " --> pdb=" O THR F 302 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N THR F 302 " --> pdb=" O TYR F 260 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 442 through 443 removed outlier: 3.748A pdb=" N LYS F 442 " --> pdb=" O ILE F 450 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'F' and resid 480 through 483 removed outlier: 6.233A pdb=" N CYS F 521 " --> pdb=" O LEU F 564 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 496 through 498 removed outlier: 3.696A pdb=" N MET F 498 " --> pdb=" O ILE F 507 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE F 507 " --> pdb=" O MET F 498 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 546 through 547 removed outlier: 3.545A pdb=" N ILE F 546 " --> pdb=" O LEU F 557 " (cutoff:3.500A) 1966 hydrogen bonds defined for protein. 5676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 143 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 113 stacking parallelities Total time for adding SS restraints: 26.86 Time building geometry restraints manager: 14.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 20414 1.34 - 1.47: 15127 1.47 - 1.61: 27705 1.61 - 1.74: 28 1.74 - 1.87: 440 Bond restraints: 63714 Sorted by residual: bond pdb=" CA ILE 5 87 " pdb=" CB ILE 5 87 " ideal model delta sigma weight residual 1.539 1.517 0.022 5.40e-03 3.43e+04 1.67e+01 bond pdb=" CA ILE D 87 " pdb=" CB ILE D 87 " ideal model delta sigma weight residual 1.539 1.517 0.022 5.40e-03 3.43e+04 1.59e+01 bond pdb=" C LEU F 343 " pdb=" N SER F 344 " ideal model delta sigma weight residual 1.331 1.251 0.080 2.83e-02 1.25e+03 8.00e+00 bond pdb=" C LEU 7 343 " pdb=" N SER 7 344 " ideal model delta sigma weight residual 1.331 1.251 0.080 2.83e-02 1.25e+03 7.96e+00 bond pdb=" C VAL E 415 " pdb=" N LYS E 416 " ideal model delta sigma weight residual 1.331 1.273 0.058 2.07e-02 2.33e+03 7.72e+00 ... (remaining 63709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 85587 4.18 - 8.35: 981 8.35 - 12.53: 116 12.53 - 16.70: 18 16.70 - 20.88: 10 Bond angle restraints: 86712 Sorted by residual: angle pdb=" N GLY 6 399 " pdb=" CA GLY 6 399 " pdb=" C GLY 6 399 " ideal model delta sigma weight residual 114.67 131.75 -17.08 1.10e+00 8.26e-01 2.41e+02 angle pdb=" N GLY E 399 " pdb=" CA GLY E 399 " pdb=" C GLY E 399 " ideal model delta sigma weight residual 114.67 131.74 -17.07 1.10e+00 8.26e-01 2.41e+02 angle pdb=" N HIS 7 620 " pdb=" CA HIS 7 620 " pdb=" C HIS 7 620 " ideal model delta sigma weight residual 114.75 100.09 14.66 1.26e+00 6.30e-01 1.35e+02 angle pdb=" N HIS F 620 " pdb=" CA HIS F 620 " pdb=" C HIS F 620 " ideal model delta sigma weight residual 114.75 100.13 14.62 1.26e+00 6.30e-01 1.35e+02 angle pdb=" C GLU 5 269 " pdb=" N MET 5 270 " pdb=" CA MET 5 270 " ideal model delta sigma weight residual 122.31 143.19 -20.88 2.34e+00 1.83e-01 7.96e+01 ... (remaining 86707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 36860 26.09 - 52.18: 1778 52.18 - 78.28: 245 78.28 - 104.37: 14 104.37 - 130.46: 3 Dihedral angle restraints: 38900 sinusoidal: 16558 harmonic: 22342 Sorted by residual: dihedral pdb=" CA ILE C 360 " pdb=" C ILE C 360 " pdb=" N ASP C 361 " pdb=" CA ASP C 361 " ideal model delta harmonic sigma weight residual 180.00 -125.34 -54.66 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA ILE 4 360 " pdb=" C ILE 4 360 " pdb=" N ASP 4 361 " pdb=" CA ASP 4 361 " ideal model delta harmonic sigma weight residual -180.00 -125.36 -54.64 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA PRO F 501 " pdb=" C PRO F 501 " pdb=" N VAL F 502 " pdb=" CA VAL F 502 " ideal model delta harmonic sigma weight residual -180.00 -127.04 -52.96 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 38897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 8054 0.077 - 0.154: 1827 0.154 - 0.230: 180 0.230 - 0.307: 17 0.307 - 0.384: 4 Chirality restraints: 10082 Sorted by residual: chirality pdb=" CG LEU A 306 " pdb=" CB LEU A 306 " pdb=" CD1 LEU A 306 " pdb=" CD2 LEU A 306 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CG LEU 2 306 " pdb=" CB LEU 2 306 " pdb=" CD1 LEU 2 306 " pdb=" CD2 LEU 2 306 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE 2 636 " pdb=" CA ILE 2 636 " pdb=" CG1 ILE 2 636 " pdb=" CG2 ILE 2 636 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 10079 not shown) Planarity restraints: 10746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 211 " 0.035 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR 3 211 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 211 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 211 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 211 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 211 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR 3 211 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR 3 211 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 211 " 0.034 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR B 211 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR B 211 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 211 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 211 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 211 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 211 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 211 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 461 " -0.056 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO F 462 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO F 462 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO F 462 " -0.043 5.00e-02 4.00e+02 ... (remaining 10743 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 11484 2.77 - 3.30: 56662 3.30 - 3.83: 96017 3.83 - 4.37: 104374 4.37 - 4.90: 176546 Nonbonded interactions: 445083 Sorted by model distance: nonbonded pdb=" OH TYR F 482 " pdb=" OD2 ASP F 524 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR 7 482 " pdb=" OD2 ASP 7 524 " model vdw 2.234 3.040 nonbonded pdb=" O HIS 3 564 " pdb=" OG1 THR 3 568 " model vdw 2.243 3.040 nonbonded pdb=" O HIS B 564 " pdb=" OG1 THR B 568 " model vdw 2.244 3.040 nonbonded pdb=" O VAL F 616 " pdb=" O VAL F 619 " model vdw 2.245 2.432 ... (remaining 445078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '2' selection = chain 'A' } ncs_group { reference = chain '3' selection = chain 'B' } ncs_group { reference = chain '4' selection = chain 'C' } ncs_group { reference = chain '5' selection = chain 'D' } ncs_group { reference = chain '6' selection = chain 'E' } ncs_group { reference = chain '7' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 1.990 Check model and map are aligned: 0.360 Set scattering table: 0.470 Process input model: 123.230 Find NCS groups from input model: 4.390 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 63714 Z= 0.545 Angle : 1.239 20.878 86712 Z= 0.671 Chirality : 0.063 0.384 10082 Planarity : 0.007 0.085 10746 Dihedral : 14.591 130.462 24350 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.22 % Favored : 87.63 % Rotamer: Outliers : 1.24 % Allowed : 5.08 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.30 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.07), residues: 7548 helix: -3.23 (0.07), residues: 2542 sheet: -2.71 (0.15), residues: 1018 loop : -3.35 (0.08), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 181 HIS 0.020 0.003 HIS 4 723 PHE 0.041 0.004 PHE D 31 TYR 0.062 0.003 TYR 3 211 ARG 0.016 0.001 ARG 6 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1750 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1666 time to evaluate : 5.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: D residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 614 ASP cc_start: 0.7424 (m-30) cc_final: 0.7200 (t0) REVERT: 2 622 GLU cc_start: 0.8216 (tp30) cc_final: 0.7767 (tp30) REVERT: 3 97 ILE cc_start: 0.9222 (mt) cc_final: 0.8817 (pt) REVERT: 3 177 ASN cc_start: 0.8942 (t0) cc_final: 0.8634 (t0) REVERT: 3 275 ASP cc_start: 0.9013 (p0) cc_final: 0.8790 (p0) REVERT: 3 279 ASP cc_start: 0.7800 (m-30) cc_final: 0.7535 (m-30) REVERT: 3 307 ASN cc_start: 0.8581 (t0) cc_final: 0.8284 (t0) REVERT: 3 330 HIS cc_start: 0.8011 (t-170) cc_final: 0.6728 (p-80) REVERT: 3 346 ASP cc_start: 0.7400 (m-30) cc_final: 0.6809 (m-30) REVERT: 3 535 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8777 (pp) REVERT: 4 229 GLN cc_start: 0.7610 (mt0) cc_final: 0.7404 (tm-30) REVERT: 4 273 ASP cc_start: 0.8501 (m-30) cc_final: 0.8140 (m-30) REVERT: 4 538 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8476 (tptt) REVERT: 4 610 ASP cc_start: 0.7516 (p0) cc_final: 0.7212 (p0) REVERT: 4 654 ILE cc_start: 0.9289 (mt) cc_final: 0.9067 (mp) REVERT: 4 780 MET cc_start: 0.7508 (mmp) cc_final: 0.7239 (mpp) REVERT: 5 65 MET cc_start: 0.8206 (ttp) cc_final: 0.6677 (ttp) REVERT: 5 234 LYS cc_start: 0.6822 (pptt) cc_final: 0.6136 (ptpt) REVERT: 5 390 CYS cc_start: 0.8331 (p) cc_final: 0.8004 (m) REVERT: 5 458 MET cc_start: 0.7221 (ptp) cc_final: 0.6853 (ppp) REVERT: 5 465 GLU cc_start: 0.8165 (tp30) cc_final: 0.7812 (tp30) REVERT: 5 517 THR cc_start: 0.9260 (p) cc_final: 0.8970 (p) REVERT: 5 689 MET cc_start: 0.8439 (mmm) cc_final: 0.8029 (mtt) REVERT: 6 148 LEU cc_start: 0.7854 (mt) cc_final: 0.7641 (pp) REVERT: 6 175 TYR cc_start: 0.8518 (t80) cc_final: 0.8113 (t80) REVERT: 6 278 ASP cc_start: 0.8191 (t0) cc_final: 0.7573 (t0) REVERT: 6 514 ASN cc_start: 0.8565 (m-40) cc_final: 0.8215 (t0) REVERT: 6 525 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8150 (pt) REVERT: 6 636 CYS cc_start: 0.8424 (t) cc_final: 0.7913 (p) REVERT: 6 805 ARG cc_start: 0.8306 (ptp-170) cc_final: 0.8015 (mtm180) REVERT: 7 1 MET cc_start: 0.3705 (ttp) cc_final: 0.2809 (mmm) REVERT: 7 288 GLU cc_start: 0.7435 (tt0) cc_final: 0.6947 (tm-30) REVERT: 7 298 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8889 (pp) REVERT: 7 526 PHE cc_start: 0.8616 (t80) cc_final: 0.8407 (t80) REVERT: 7 602 ASP cc_start: 0.7011 (t0) cc_final: 0.6410 (p0) REVERT: 7 644 TYR cc_start: 0.8984 (t80) cc_final: 0.8727 (t80) REVERT: 7 675 MET cc_start: 0.6513 (mtt) cc_final: 0.6005 (ttt) REVERT: A 622 GLU cc_start: 0.8348 (tp30) cc_final: 0.7660 (tp30) REVERT: B 97 ILE cc_start: 0.9170 (mt) cc_final: 0.8930 (mm) REVERT: B 279 ASP cc_start: 0.7911 (m-30) cc_final: 0.7629 (m-30) REVERT: B 287 LYS cc_start: 0.8974 (pttm) cc_final: 0.8773 (ptpp) REVERT: B 307 ASN cc_start: 0.8634 (t0) cc_final: 0.8380 (t0) REVERT: B 346 ASP cc_start: 0.7351 (m-30) cc_final: 0.7112 (m-30) REVERT: C 229 GLN cc_start: 0.7594 (mt0) cc_final: 0.7240 (tm-30) REVERT: C 273 ASP cc_start: 0.8540 (m-30) cc_final: 0.8237 (m-30) REVERT: C 341 ASP cc_start: 0.7882 (t0) cc_final: 0.7666 (t0) REVERT: C 349 CYS cc_start: 0.7565 (m) cc_final: 0.7190 (m) REVERT: C 462 ASP cc_start: 0.8392 (t0) cc_final: 0.8058 (t0) REVERT: C 538 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8483 (tptt) REVERT: C 654 ILE cc_start: 0.9344 (mt) cc_final: 0.9136 (mp) REVERT: C 780 MET cc_start: 0.7168 (mmp) cc_final: 0.6776 (mmm) REVERT: D 65 MET cc_start: 0.8195 (ttp) cc_final: 0.6810 (ttp) REVERT: D 234 LYS cc_start: 0.6659 (pptt) cc_final: 0.5932 (ptpt) REVERT: D 390 CYS cc_start: 0.8514 (p) cc_final: 0.8016 (m) REVERT: D 458 MET cc_start: 0.7203 (ptp) cc_final: 0.6805 (ppp) REVERT: D 469 MET cc_start: 0.9074 (mmt) cc_final: 0.8732 (mmt) REVERT: D 484 LYS cc_start: 0.8033 (mptt) cc_final: 0.7558 (mptt) REVERT: D 517 THR cc_start: 0.9346 (p) cc_final: 0.8915 (p) REVERT: D 689 MET cc_start: 0.8475 (mmm) cc_final: 0.8213 (mtt) REVERT: E 175 TYR cc_start: 0.8478 (t80) cc_final: 0.8111 (t80) REVERT: E 278 ASP cc_start: 0.8119 (t0) cc_final: 0.7540 (t0) REVERT: E 514 ASN cc_start: 0.8471 (m-40) cc_final: 0.8167 (t0) REVERT: E 525 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8178 (pt) REVERT: E 621 TYR cc_start: 0.5080 (p90) cc_final: 0.4619 (p90) REVERT: E 636 CYS cc_start: 0.8549 (t) cc_final: 0.7963 (p) REVERT: F 1 MET cc_start: 0.3680 (ttp) cc_final: 0.2793 (mmm) REVERT: F 276 ARG cc_start: 0.8352 (tpp-160) cc_final: 0.8130 (tpp80) REVERT: F 288 GLU cc_start: 0.7505 (tt0) cc_final: 0.6985 (tm-30) REVERT: F 298 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8876 (pp) REVERT: F 453 ASP cc_start: 0.7437 (t0) cc_final: 0.7044 (p0) REVERT: F 541 MET cc_start: 0.8550 (mmt) cc_final: 0.8280 (mmm) REVERT: F 599 LEU cc_start: 0.8432 (pp) cc_final: 0.8224 (tt) REVERT: F 675 MET cc_start: 0.6503 (mtt) cc_final: 0.6007 (ttt) outliers start: 84 outliers final: 18 residues processed: 1728 average time/residue: 0.6384 time to fit residues: 1786.5946 Evaluate side-chains 867 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 844 time to evaluate : 5.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 535 LEU Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 325 THR Chi-restraints excluded: chain 5 residue 326 PRO Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 279 THR Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 464 VAL Chi-restraints excluded: chain 7 residue 476 ILE Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 326 PRO Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 464 VAL Chi-restraints excluded: chain F residue 476 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 650 optimal weight: 0.9990 chunk 583 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 393 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 603 optimal weight: 2.9990 chunk 233 optimal weight: 30.0000 chunk 366 optimal weight: 4.9990 chunk 449 optimal weight: 0.9980 chunk 699 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 528 ASN 2 653 ASN 2 768 HIS 2 856 GLN 3 51 ASN 3 310 ASN 3 312 ASN 3 424 ASN 3 522 GLN 3 691 ASN 4 318 ASN 4 400 GLN 4 465 HIS ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 651 GLN 4 723 HIS 4 735 HIS ** 5 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 411 ASN 5 500 GLN 5 676 HIS 6 366 ASN ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 570 ASN 6 750 GLN 7 68 GLN 7 89 GLN 7 229 GLN 7 334 HIS 7 384 HIS 7 425 ASN 7 543 GLN 7 544 GLN A 653 ASN A 768 HIS A 856 GLN B 51 ASN B 310 ASN B 312 ASN B 424 ASN B 691 ASN C 318 ASN C 400 GLN C 465 HIS ** C 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN C 723 HIS C 735 HIS ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 GLN D 676 HIS E 366 ASN E 409 GLN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 ASN E 700 ASN E 750 GLN F 68 GLN F 89 GLN F 229 GLN F 334 HIS F 384 HIS F 425 ASN F 543 GLN F 544 GLN ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 63714 Z= 0.213 Angle : 0.793 12.650 86712 Z= 0.411 Chirality : 0.046 0.270 10082 Planarity : 0.005 0.068 10746 Dihedral : 15.166 127.107 9774 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.80 % Favored : 90.13 % Rotamer: Outliers : 3.33 % Allowed : 12.20 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.08), residues: 7548 helix: -1.28 (0.09), residues: 2634 sheet: -2.45 (0.15), residues: 1052 loop : -2.94 (0.09), residues: 3862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 111 HIS 0.013 0.001 HIS 7 615 PHE 0.024 0.002 PHE 5 38 TYR 0.023 0.002 TYR B 211 ARG 0.008 0.001 ARG 6 696 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1014 time to evaluate : 5.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 279 THR cc_start: 0.7963 (m) cc_final: 0.7701 (p) REVERT: 2 302 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7782 (p) REVERT: 2 644 CYS cc_start: 0.8153 (m) cc_final: 0.7927 (m) REVERT: 3 97 ILE cc_start: 0.9177 (mt) cc_final: 0.8886 (mm) REVERT: 3 117 GLU cc_start: 0.8336 (pt0) cc_final: 0.8078 (pt0) REVERT: 3 185 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9127 (mt) REVERT: 3 279 ASP cc_start: 0.7767 (m-30) cc_final: 0.7397 (m-30) REVERT: 3 307 ASN cc_start: 0.8546 (t0) cc_final: 0.8317 (t0) REVERT: 3 325 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9041 (m) REVERT: 3 330 HIS cc_start: 0.7957 (t-170) cc_final: 0.6630 (p-80) REVERT: 3 346 ASP cc_start: 0.7233 (m-30) cc_final: 0.6819 (m-30) REVERT: 3 364 SER cc_start: 0.9067 (m) cc_final: 0.8817 (p) REVERT: 3 482 ASP cc_start: 0.8102 (p0) cc_final: 0.7628 (m-30) REVERT: 3 497 ILE cc_start: 0.8595 (mp) cc_final: 0.8318 (mm) REVERT: 3 535 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8541 (pp) REVERT: 3 685 ASP cc_start: 0.8317 (t0) cc_final: 0.8081 (t0) REVERT: 4 206 ARG cc_start: 0.8718 (mmt90) cc_final: 0.8498 (mpt180) REVERT: 4 229 GLN cc_start: 0.7541 (mt0) cc_final: 0.7241 (tm-30) REVERT: 4 273 ASP cc_start: 0.8479 (m-30) cc_final: 0.8206 (m-30) REVERT: 4 473 ARG cc_start: 0.8496 (mmm160) cc_final: 0.8172 (mmm160) REVERT: 4 506 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8528 (tm) REVERT: 4 702 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8498 (m-10) REVERT: 4 728 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7220 (t80) REVERT: 4 780 MET cc_start: 0.7393 (mmp) cc_final: 0.7021 (mmm) REVERT: 5 65 MET cc_start: 0.7553 (ttp) cc_final: 0.7236 (ttp) REVERT: 5 76 TYR cc_start: 0.7635 (t80) cc_final: 0.7137 (t80) REVERT: 5 234 LYS cc_start: 0.6780 (pptt) cc_final: 0.6171 (ptpt) REVERT: 5 465 GLU cc_start: 0.8155 (tp30) cc_final: 0.7595 (tp30) REVERT: 5 469 MET cc_start: 0.8823 (mmt) cc_final: 0.8485 (mmt) REVERT: 5 513 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8552 (pp) REVERT: 5 517 THR cc_start: 0.9196 (p) cc_final: 0.8914 (p) REVERT: 5 565 ASP cc_start: 0.8949 (m-30) cc_final: 0.8632 (p0) REVERT: 5 689 MET cc_start: 0.8599 (mmm) cc_final: 0.8133 (mtt) REVERT: 6 175 TYR cc_start: 0.8381 (t80) cc_final: 0.7973 (t80) REVERT: 6 278 ASP cc_start: 0.8042 (t0) cc_final: 0.7423 (t0) REVERT: 6 379 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8777 (m) REVERT: 6 514 ASN cc_start: 0.8388 (m-40) cc_final: 0.8182 (t0) REVERT: 6 525 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8179 (pt) REVERT: 6 621 TYR cc_start: 0.4909 (p90) cc_final: 0.3794 (p90) REVERT: 6 805 ARG cc_start: 0.8094 (ptp-170) cc_final: 0.7640 (mtt180) REVERT: 7 84 ASP cc_start: 0.7809 (m-30) cc_final: 0.7504 (m-30) REVERT: 7 288 GLU cc_start: 0.7604 (tt0) cc_final: 0.7311 (tm-30) REVERT: 7 298 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8912 (pp) REVERT: 7 442 LYS cc_start: 0.7460 (tptt) cc_final: 0.6913 (tttt) REVERT: 7 529 MET cc_start: 0.8570 (mmt) cc_final: 0.8046 (mmt) REVERT: 7 533 ASP cc_start: 0.8596 (t70) cc_final: 0.8367 (t70) REVERT: 7 675 MET cc_start: 0.6183 (mtt) cc_final: 0.5761 (ttt) REVERT: A 279 THR cc_start: 0.7990 (m) cc_final: 0.7721 (p) REVERT: A 302 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7699 (p) REVERT: A 609 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7306 (m-10) REVERT: A 622 GLU cc_start: 0.8128 (tp30) cc_final: 0.7905 (tp30) REVERT: A 628 SER cc_start: 0.8638 (p) cc_final: 0.8280 (m) REVERT: B 117 GLU cc_start: 0.8242 (pt0) cc_final: 0.8020 (pt0) REVERT: B 234 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6792 (mm-30) REVERT: B 279 ASP cc_start: 0.7751 (m-30) cc_final: 0.7457 (m-30) REVERT: B 325 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.8992 (m) REVERT: B 346 ASP cc_start: 0.7391 (m-30) cc_final: 0.7063 (m-30) REVERT: B 364 SER cc_start: 0.8907 (m) cc_final: 0.8642 (p) REVERT: B 407 MET cc_start: 0.7648 (mtp) cc_final: 0.7388 (mtp) REVERT: B 490 MET cc_start: 0.8486 (tpp) cc_final: 0.8224 (tpp) REVERT: B 522 GLN cc_start: 0.8169 (mp10) cc_final: 0.7477 (tm-30) REVERT: C 229 GLN cc_start: 0.7489 (mt0) cc_final: 0.7237 (tm-30) REVERT: C 273 ASP cc_start: 0.8528 (m-30) cc_final: 0.8246 (m-30) REVERT: C 462 ASP cc_start: 0.8537 (t0) cc_final: 0.8327 (t0) REVERT: C 473 ARG cc_start: 0.8538 (mmm160) cc_final: 0.8188 (mmm160) REVERT: C 506 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8566 (tm) REVERT: C 702 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: C 746 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7948 (t80) REVERT: C 780 MET cc_start: 0.7095 (mmp) cc_final: 0.6604 (mmm) REVERT: D 65 MET cc_start: 0.7539 (ttp) cc_final: 0.7233 (ttp) REVERT: D 76 TYR cc_start: 0.7652 (t80) cc_final: 0.7163 (t80) REVERT: D 85 ASP cc_start: 0.7958 (t0) cc_final: 0.7750 (m-30) REVERT: D 234 LYS cc_start: 0.6634 (pptt) cc_final: 0.6094 (ptpt) REVERT: D 390 CYS cc_start: 0.8464 (p) cc_final: 0.8170 (m) REVERT: D 458 MET cc_start: 0.7256 (ptp) cc_final: 0.6814 (ppp) REVERT: D 465 GLU cc_start: 0.7919 (tp30) cc_final: 0.7379 (tp30) REVERT: D 469 MET cc_start: 0.8999 (mmt) cc_final: 0.8795 (mmt) REVERT: D 513 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8501 (pp) REVERT: D 681 ILE cc_start: 0.8583 (mm) cc_final: 0.8217 (mt) REVERT: D 689 MET cc_start: 0.8455 (mmm) cc_final: 0.8091 (mtt) REVERT: E 175 TYR cc_start: 0.8275 (t80) cc_final: 0.7901 (t80) REVERT: E 261 ARG cc_start: 0.3567 (mpt180) cc_final: 0.2745 (mtt90) REVERT: E 278 ASP cc_start: 0.7974 (t0) cc_final: 0.7359 (t0) REVERT: E 379 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8731 (m) REVERT: E 525 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8181 (pt) REVERT: E 621 TYR cc_start: 0.4938 (p90) cc_final: 0.4423 (p90) REVERT: E 636 CYS cc_start: 0.8594 (t) cc_final: 0.8080 (p) REVERT: E 794 ARG cc_start: 0.6664 (tpm170) cc_final: 0.6324 (tpm170) REVERT: F 84 ASP cc_start: 0.7681 (m-30) cc_final: 0.7378 (m-30) REVERT: F 288 GLU cc_start: 0.7645 (tt0) cc_final: 0.7402 (tm-30) REVERT: F 298 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8870 (pp) REVERT: F 402 MET cc_start: 0.8211 (tpp) cc_final: 0.7926 (tpp) REVERT: F 442 LYS cc_start: 0.7333 (tptt) cc_final: 0.6832 (tttt) REVERT: F 453 ASP cc_start: 0.6918 (t0) cc_final: 0.6664 (p0) REVERT: F 529 MET cc_start: 0.8553 (mmt) cc_final: 0.8072 (mmt) REVERT: F 533 ASP cc_start: 0.8492 (t70) cc_final: 0.8237 (t70) REVERT: F 541 MET cc_start: 0.8139 (mmt) cc_final: 0.7805 (mmt) REVERT: F 599 LEU cc_start: 0.8330 (pp) cc_final: 0.8076 (tt) REVERT: F 675 MET cc_start: 0.5988 (mtt) cc_final: 0.5605 (ttt) outliers start: 220 outliers final: 95 residues processed: 1168 average time/residue: 0.5690 time to fit residues: 1132.2685 Evaluate side-chains 881 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 765 time to evaluate : 5.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 347 ILE Chi-restraints excluded: chain 2 residue 675 SER Chi-restraints excluded: chain 2 residue 833 ASP Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 502 ILE Chi-restraints excluded: chain 3 residue 535 LEU Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 458 LYS Chi-restraints excluded: chain 4 residue 492 HIS Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 4 residue 728 TYR Chi-restraints excluded: chain 4 residue 729 LEU Chi-restraints excluded: chain 4 residue 756 GLU Chi-restraints excluded: chain 5 residue 23 ASP Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 325 THR Chi-restraints excluded: chain 5 residue 377 SER Chi-restraints excluded: chain 5 residue 478 CYS Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 594 ILE Chi-restraints excluded: chain 5 residue 632 GLN Chi-restraints excluded: chain 6 residue 122 PHE Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 742 ILE Chi-restraints excluded: chain 7 residue 25 LEU Chi-restraints excluded: chain 7 residue 83 ASP Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 279 THR Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 374 THR Chi-restraints excluded: chain 7 residue 416 LYS Chi-restraints excluded: chain 7 residue 464 VAL Chi-restraints excluded: chain 7 residue 476 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 497 VAL Chi-restraints excluded: chain 7 residue 507 ILE Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 642 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 702 PHE Chi-restraints excluded: chain C residue 746 PHE Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 576 HIS Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 796 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 464 VAL Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 507 ILE Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 601 LEU Chi-restraints excluded: chain F residue 642 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 388 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 581 optimal weight: 6.9990 chunk 476 optimal weight: 10.0000 chunk 192 optimal weight: 0.1980 chunk 700 optimal weight: 20.0000 chunk 756 optimal weight: 0.3980 chunk 623 optimal weight: 7.9990 chunk 694 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 561 optimal weight: 8.9990 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 51 ASN 4 410 GLN 4 413 HIS 4 493 ASN 4 549 ASN ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 409 GLN 6 700 ASN 6 799 GLN B 51 ASN ** B 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN C 493 ASN ** C 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN E 669 HIS E 700 ASN E 799 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 63714 Z= 0.330 Angle : 0.800 12.496 86712 Z= 0.416 Chirality : 0.047 0.243 10082 Planarity : 0.005 0.068 10746 Dihedral : 15.014 129.472 9772 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.37 % Favored : 88.61 % Rotamer: Outliers : 4.45 % Allowed : 14.27 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.36 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.09), residues: 7548 helix: -0.32 (0.10), residues: 2654 sheet: -2.29 (0.15), residues: 1074 loop : -2.89 (0.09), residues: 3820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 111 HIS 0.012 0.002 HIS F 622 PHE 0.027 0.002 PHE D 31 TYR 0.024 0.002 TYR 3 211 ARG 0.012 0.001 ARG 4 607 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 796 time to evaluate : 5.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 279 THR cc_start: 0.8045 (m) cc_final: 0.7812 (p) REVERT: 2 302 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7761 (t) REVERT: 2 644 CYS cc_start: 0.8174 (m) cc_final: 0.7956 (m) REVERT: 3 97 ILE cc_start: 0.9248 (mt) cc_final: 0.8904 (pt) REVERT: 3 117 GLU cc_start: 0.8585 (pt0) cc_final: 0.8318 (pt0) REVERT: 3 234 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7211 (mm-30) REVERT: 3 279 ASP cc_start: 0.7798 (m-30) cc_final: 0.7410 (m-30) REVERT: 3 346 ASP cc_start: 0.7434 (m-30) cc_final: 0.7002 (m-30) REVERT: 3 364 SER cc_start: 0.9062 (m) cc_final: 0.8818 (p) REVERT: 3 482 ASP cc_start: 0.8169 (p0) cc_final: 0.7303 (t0) REVERT: 3 535 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8566 (pp) REVERT: 4 206 ARG cc_start: 0.8828 (mmt90) cc_final: 0.8553 (mpt180) REVERT: 4 229 GLN cc_start: 0.7714 (mt0) cc_final: 0.7416 (tm-30) REVERT: 4 273 ASP cc_start: 0.8503 (m-30) cc_final: 0.8189 (m-30) REVERT: 4 456 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8972 (tt) REVERT: 4 473 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8558 (mmm160) REVERT: 4 561 ASP cc_start: 0.6852 (t0) cc_final: 0.6623 (p0) REVERT: 4 633 GLU cc_start: 0.8098 (tp30) cc_final: 0.7792 (tp30) REVERT: 4 702 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8588 (m-10) REVERT: 4 728 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7189 (t80) REVERT: 4 780 MET cc_start: 0.7424 (mmp) cc_final: 0.6939 (mmm) REVERT: 5 65 MET cc_start: 0.7857 (ttp) cc_final: 0.7623 (ttp) REVERT: 5 76 TYR cc_start: 0.8119 (t80) cc_final: 0.7731 (t80) REVERT: 5 234 LYS cc_start: 0.7003 (pptt) cc_final: 0.6377 (ptpt) REVERT: 5 331 LEU cc_start: 0.7872 (pt) cc_final: 0.7672 (pp) REVERT: 5 449 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8005 (tt) REVERT: 5 465 GLU cc_start: 0.8289 (tp30) cc_final: 0.7606 (tp30) REVERT: 5 469 MET cc_start: 0.8821 (mmt) cc_final: 0.8537 (mmt) REVERT: 5 513 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8692 (pp) REVERT: 5 689 MET cc_start: 0.8688 (mmm) cc_final: 0.8151 (mtt) REVERT: 6 175 TYR cc_start: 0.8599 (t80) cc_final: 0.8250 (t80) REVERT: 6 261 ARG cc_start: 0.3242 (mpt180) cc_final: 0.2652 (mtt90) REVERT: 6 379 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8745 (m) REVERT: 6 525 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8243 (pt) REVERT: 6 805 ARG cc_start: 0.8187 (ptp-170) cc_final: 0.7810 (mtt180) REVERT: 7 1 MET cc_start: 0.4774 (ptm) cc_final: 0.4155 (ptm) REVERT: 7 64 MET cc_start: 0.8565 (mmp) cc_final: 0.8365 (mmp) REVERT: 7 160 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8302 (tm-30) REVERT: 7 288 GLU cc_start: 0.7773 (tt0) cc_final: 0.7516 (tm-30) REVERT: 7 298 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8990 (pp) REVERT: 7 402 MET cc_start: 0.8397 (tpp) cc_final: 0.7839 (tpp) REVERT: 7 442 LYS cc_start: 0.7412 (tptt) cc_final: 0.6991 (tttt) REVERT: 7 525 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8328 (mm-30) REVERT: 7 644 TYR cc_start: 0.9100 (t80) cc_final: 0.8757 (t80) REVERT: 7 675 MET cc_start: 0.6070 (mtt) cc_final: 0.5569 (ttt) REVERT: A 279 THR cc_start: 0.8074 (m) cc_final: 0.7828 (p) REVERT: A 302 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7754 (t) REVERT: A 581 ARG cc_start: 0.7817 (ptp90) cc_final: 0.7142 (ttp80) REVERT: A 646 ILE cc_start: 0.9351 (mt) cc_final: 0.9130 (tt) REVERT: B 29 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 234 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7155 (mm-30) REVERT: B 240 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8633 (mmmm) REVERT: B 261 MET cc_start: 0.8247 (ttp) cc_final: 0.8008 (ptp) REVERT: B 279 ASP cc_start: 0.7876 (m-30) cc_final: 0.7491 (m-30) REVERT: B 346 ASP cc_start: 0.7426 (m-30) cc_final: 0.7081 (m-30) REVERT: B 364 SER cc_start: 0.9044 (m) cc_final: 0.8805 (p) REVERT: B 482 ASP cc_start: 0.8099 (p0) cc_final: 0.7579 (m-30) REVERT: C 229 GLN cc_start: 0.7673 (mt0) cc_final: 0.7401 (tm-30) REVERT: C 273 ASP cc_start: 0.8640 (m-30) cc_final: 0.8330 (m-30) REVERT: C 456 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8953 (tt) REVERT: C 473 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8559 (mmm160) REVERT: C 506 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8630 (tm) REVERT: C 702 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8415 (m-10) REVERT: C 728 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7262 (t80) REVERT: C 746 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.8124 (t80) REVERT: C 780 MET cc_start: 0.7220 (mmp) cc_final: 0.6709 (mmm) REVERT: D 31 PHE cc_start: 0.8166 (m-80) cc_final: 0.7732 (m-10) REVERT: D 76 TYR cc_start: 0.8094 (t80) cc_final: 0.7808 (t80) REVERT: D 85 ASP cc_start: 0.7951 (t0) cc_final: 0.7711 (t0) REVERT: D 205 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8411 (m) REVERT: D 234 LYS cc_start: 0.6636 (pptt) cc_final: 0.6101 (ptpt) REVERT: D 260 GLU cc_start: 0.7914 (tp30) cc_final: 0.7677 (tp30) REVERT: D 329 LYS cc_start: 0.8478 (tptp) cc_final: 0.8199 (mtmm) REVERT: D 458 MET cc_start: 0.7296 (ptp) cc_final: 0.6923 (ppp) REVERT: D 465 GLU cc_start: 0.8214 (tp30) cc_final: 0.7954 (tp30) REVERT: D 469 MET cc_start: 0.9023 (mmt) cc_final: 0.8804 (mmt) REVERT: D 513 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8663 (pp) REVERT: D 689 MET cc_start: 0.8571 (mmm) cc_final: 0.8179 (mtt) REVERT: E 175 TYR cc_start: 0.8563 (t80) cc_final: 0.8243 (t80) REVERT: E 261 ARG cc_start: 0.3962 (mpt180) cc_final: 0.3360 (mtt90) REVERT: E 379 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8712 (m) REVERT: E 525 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.7698 (tp) REVERT: E 636 CYS cc_start: 0.8544 (t) cc_final: 0.8170 (p) REVERT: E 641 PHE cc_start: 0.6441 (OUTLIER) cc_final: 0.6223 (m-80) REVERT: F 1 MET cc_start: 0.4647 (ptm) cc_final: 0.4047 (ptm) REVERT: F 298 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8955 (pp) REVERT: F 442 LYS cc_start: 0.7226 (tptt) cc_final: 0.6741 (tttt) REVERT: F 533 ASP cc_start: 0.8654 (t70) cc_final: 0.8376 (t70) REVERT: F 675 MET cc_start: 0.6009 (mtt) cc_final: 0.5633 (ttt) REVERT: F 717 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9316 (mm) outliers start: 294 outliers final: 174 residues processed: 1008 average time/residue: 0.5552 time to fit residues: 976.0300 Evaluate side-chains 897 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 699 time to evaluate : 5.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 347 ILE Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 455 SER Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 556 VAL Chi-restraints excluded: chain 2 residue 597 VAL Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 675 SER Chi-restraints excluded: chain 2 residue 806 THR Chi-restraints excluded: chain 2 residue 833 ASP Chi-restraints excluded: chain 3 residue 45 ILE Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 362 ILE Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 3 residue 489 VAL Chi-restraints excluded: chain 3 residue 502 ILE Chi-restraints excluded: chain 3 residue 535 LEU Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 348 LYS Chi-restraints excluded: chain 4 residue 389 CYS Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 456 LEU Chi-restraints excluded: chain 4 residue 458 LYS Chi-restraints excluded: chain 4 residue 485 LEU Chi-restraints excluded: chain 4 residue 492 HIS Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 4 residue 564 ILE Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 616 LEU Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 4 residue 728 TYR Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 349 PHE Chi-restraints excluded: chain 5 residue 377 SER Chi-restraints excluded: chain 5 residue 410 ILE Chi-restraints excluded: chain 5 residue 444 SER Chi-restraints excluded: chain 5 residue 449 LEU Chi-restraints excluded: chain 5 residue 478 CYS Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 575 ILE Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 594 ILE Chi-restraints excluded: chain 5 residue 631 LYS Chi-restraints excluded: chain 5 residue 632 GLN Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 348 VAL Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 457 CYS Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 742 ILE Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 83 ASP Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 269 VAL Chi-restraints excluded: chain 7 residue 279 THR Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 416 LYS Chi-restraints excluded: chain 7 residue 464 VAL Chi-restraints excluded: chain 7 residue 476 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 491 VAL Chi-restraints excluded: chain 7 residue 497 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 590 LEU Chi-restraints excluded: chain 7 residue 601 LEU Chi-restraints excluded: chain 7 residue 642 ILE Chi-restraints excluded: chain 7 residue 690 LEU Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 702 PHE Chi-restraints excluded: chain C residue 728 TYR Chi-restraints excluded: chain C residue 746 PHE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 349 PHE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 478 CYS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 457 CYS Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 598 THR Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 641 PHE Chi-restraints excluded: chain E residue 742 ILE Chi-restraints excluded: chain E residue 751 LEU Chi-restraints excluded: chain E residue 796 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 464 VAL Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain F residue 601 LEU Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain F residue 696 SER Chi-restraints excluded: chain F residue 712 ASP Chi-restraints excluded: chain F residue 717 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 692 optimal weight: 0.7980 chunk 526 optimal weight: 3.9990 chunk 363 optimal weight: 30.0000 chunk 77 optimal weight: 0.5980 chunk 334 optimal weight: 0.9980 chunk 470 optimal weight: 10.0000 chunk 703 optimal weight: 0.8980 chunk 744 optimal weight: 9.9990 chunk 367 optimal weight: 0.0060 chunk 666 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 849 GLN 3 51 ASN ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 576 HIS ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS 6 700 ASN A 849 GLN B 51 ASN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 HIS ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 669 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 63714 Z= 0.171 Angle : 0.711 12.768 86712 Z= 0.364 Chirality : 0.044 0.239 10082 Planarity : 0.004 0.062 10746 Dihedral : 14.663 127.006 9770 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.66 % Favored : 91.31 % Rotamer: Outliers : 3.98 % Allowed : 15.89 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.41 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.09), residues: 7548 helix: 0.26 (0.10), residues: 2666 sheet: -2.07 (0.16), residues: 1056 loop : -2.72 (0.09), residues: 3826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.006 0.001 HIS B 569 PHE 0.017 0.001 PHE D 38 TYR 0.015 0.001 TYR 7 482 ARG 0.010 0.000 ARG 5 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 850 time to evaluate : 5.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 279 THR cc_start: 0.7984 (m) cc_final: 0.7767 (p) REVERT: 2 302 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7553 (p) REVERT: 2 581 ARG cc_start: 0.7747 (ptp90) cc_final: 0.7118 (ttp80) REVERT: 2 781 MET cc_start: 0.7540 (mtt) cc_final: 0.7134 (ptt) REVERT: 3 34 THR cc_start: 0.7645 (m) cc_final: 0.7172 (m) REVERT: 3 97 ILE cc_start: 0.9143 (mt) cc_final: 0.8888 (mm) REVERT: 3 117 GLU cc_start: 0.8475 (pt0) cc_final: 0.8198 (pt0) REVERT: 3 191 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8059 (mt) REVERT: 3 234 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7073 (mm-30) REVERT: 3 261 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7757 (ptp) REVERT: 3 264 MET cc_start: 0.8008 (mtt) cc_final: 0.7164 (mtt) REVERT: 3 279 ASP cc_start: 0.7693 (m-30) cc_final: 0.7326 (m-30) REVERT: 3 325 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9071 (m) REVERT: 3 330 HIS cc_start: 0.7999 (t-170) cc_final: 0.6757 (p-80) REVERT: 3 346 ASP cc_start: 0.7343 (m-30) cc_final: 0.6902 (m-30) REVERT: 3 407 MET cc_start: 0.7765 (mtp) cc_final: 0.7461 (mtp) REVERT: 3 535 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8479 (pp) REVERT: 4 206 ARG cc_start: 0.8746 (mmt90) cc_final: 0.8491 (mpt180) REVERT: 4 229 GLN cc_start: 0.7709 (mt0) cc_final: 0.7456 (tm-30) REVERT: 4 273 ASP cc_start: 0.8481 (m-30) cc_final: 0.8150 (m-30) REVERT: 4 473 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8473 (mmm160) REVERT: 4 561 ASP cc_start: 0.6799 (t0) cc_final: 0.6528 (p0) REVERT: 4 702 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8450 (m-10) REVERT: 4 728 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7210 (t80) REVERT: 4 780 MET cc_start: 0.7356 (mmp) cc_final: 0.6913 (mmm) REVERT: 5 44 PHE cc_start: 0.6986 (p90) cc_final: 0.6608 (p90) REVERT: 5 65 MET cc_start: 0.7698 (ttp) cc_final: 0.7092 (ttp) REVERT: 5 76 TYR cc_start: 0.8020 (t80) cc_final: 0.7392 (t80) REVERT: 5 218 GLU cc_start: 0.5276 (OUTLIER) cc_final: 0.2782 (mt-10) REVERT: 5 234 LYS cc_start: 0.6717 (pptt) cc_final: 0.6122 (ptpt) REVERT: 5 260 GLU cc_start: 0.7399 (pm20) cc_final: 0.7160 (pm20) REVERT: 5 465 GLU cc_start: 0.8138 (tp30) cc_final: 0.7796 (tp30) REVERT: 5 469 MET cc_start: 0.8867 (mmt) cc_final: 0.8641 (mmt) REVERT: 5 513 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8436 (pp) REVERT: 5 689 MET cc_start: 0.8686 (mmm) cc_final: 0.8102 (mtt) REVERT: 6 175 TYR cc_start: 0.8417 (t80) cc_final: 0.8062 (t80) REVERT: 6 261 ARG cc_start: 0.3430 (mpt180) cc_final: 0.2646 (mtt90) REVERT: 6 379 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8726 (m) REVERT: 6 525 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8191 (pt) REVERT: 6 646 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6101 (mm) REVERT: 6 794 ARG cc_start: 0.6835 (tpt90) cc_final: 0.6322 (tpm170) REVERT: 6 805 ARG cc_start: 0.7986 (ptp-170) cc_final: 0.7784 (mtt180) REVERT: 7 1 MET cc_start: 0.4671 (ptm) cc_final: 0.4023 (ptm) REVERT: 7 64 MET cc_start: 0.8517 (mmp) cc_final: 0.8287 (mmp) REVERT: 7 84 ASP cc_start: 0.7721 (m-30) cc_final: 0.7415 (m-30) REVERT: 7 288 GLU cc_start: 0.7561 (tt0) cc_final: 0.7357 (tm-30) REVERT: 7 298 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8934 (pp) REVERT: 7 393 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6950 (tt) REVERT: 7 402 MET cc_start: 0.8333 (tpp) cc_final: 0.7880 (tpp) REVERT: 7 442 LYS cc_start: 0.7316 (tptt) cc_final: 0.6806 (tttt) REVERT: 7 609 ASP cc_start: 0.8161 (m-30) cc_final: 0.7940 (m-30) REVERT: 7 675 MET cc_start: 0.6005 (mtt) cc_final: 0.5624 (ttt) REVERT: A 279 THR cc_start: 0.8018 (m) cc_final: 0.7781 (p) REVERT: A 302 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7669 (t) REVERT: A 646 ILE cc_start: 0.9318 (mt) cc_final: 0.9084 (tt) REVERT: B 234 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6793 (mm-30) REVERT: B 279 ASP cc_start: 0.7709 (m-30) cc_final: 0.7338 (m-30) REVERT: B 346 ASP cc_start: 0.7325 (m-30) cc_final: 0.6983 (m-30) REVERT: B 490 MET cc_start: 0.8796 (tpp) cc_final: 0.8520 (tpp) REVERT: B 522 GLN cc_start: 0.8178 (mp10) cc_final: 0.7588 (tm-30) REVERT: B 535 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8577 (pp) REVERT: C 229 GLN cc_start: 0.7618 (mt0) cc_final: 0.7337 (tm-30) REVERT: C 273 ASP cc_start: 0.8470 (m-30) cc_final: 0.8193 (m-30) REVERT: C 561 ASP cc_start: 0.6902 (t0) cc_final: 0.6489 (p0) REVERT: C 728 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7334 (t80) REVERT: C 780 MET cc_start: 0.7294 (mmp) cc_final: 0.6765 (mmm) REVERT: C 803 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7051 (ptp-170) REVERT: D 76 TYR cc_start: 0.8000 (t80) cc_final: 0.7342 (t80) REVERT: D 205 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8422 (m) REVERT: D 218 GLU cc_start: 0.5058 (OUTLIER) cc_final: 0.2624 (mt-10) REVERT: D 234 LYS cc_start: 0.6545 (pptt) cc_final: 0.5883 (ptpt) REVERT: D 260 GLU cc_start: 0.7908 (tp30) cc_final: 0.7697 (tp30) REVERT: D 329 LYS cc_start: 0.8573 (tptp) cc_final: 0.8217 (mtmm) REVERT: D 458 MET cc_start: 0.7270 (ptp) cc_final: 0.6937 (ppp) REVERT: D 465 GLU cc_start: 0.7924 (tp30) cc_final: 0.7475 (tp30) REVERT: D 469 MET cc_start: 0.8973 (mmt) cc_final: 0.8724 (mmt) REVERT: D 513 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8567 (pp) REVERT: D 594 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6123 (mm) REVERT: D 599 MET cc_start: 0.8698 (mmm) cc_final: 0.8495 (tpp) REVERT: D 689 MET cc_start: 0.8573 (mmm) cc_final: 0.8100 (mtt) REVERT: E 175 TYR cc_start: 0.8332 (t80) cc_final: 0.7987 (t80) REVERT: E 261 ARG cc_start: 0.4065 (mpt180) cc_final: 0.3058 (mtt90) REVERT: E 278 ASP cc_start: 0.8120 (t0) cc_final: 0.7643 (t0) REVERT: E 379 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8701 (m) REVERT: E 525 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8066 (pt) REVERT: E 636 CYS cc_start: 0.8502 (t) cc_final: 0.8126 (p) REVERT: E 646 ILE cc_start: 0.6094 (OUTLIER) cc_final: 0.5743 (mm) REVERT: F 1 MET cc_start: 0.4488 (ptm) cc_final: 0.3940 (ptm) REVERT: F 64 MET cc_start: 0.8514 (mmp) cc_final: 0.8296 (mmp) REVERT: F 84 ASP cc_start: 0.7490 (m-30) cc_final: 0.7122 (m-30) REVERT: F 298 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8885 (pp) REVERT: F 393 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6929 (tt) REVERT: F 442 LYS cc_start: 0.7157 (tptt) cc_final: 0.6634 (tttt) REVERT: F 525 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8175 (mm-30) REVERT: F 541 MET cc_start: 0.8245 (mmt) cc_final: 0.7900 (mmt) REVERT: F 675 MET cc_start: 0.5958 (mtt) cc_final: 0.5625 (ttt) outliers start: 263 outliers final: 152 residues processed: 1035 average time/residue: 0.5527 time to fit residues: 992.3218 Evaluate side-chains 898 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 719 time to evaluate : 5.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 205 ARG Chi-restraints excluded: chain 2 residue 276 MET Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 347 ILE Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 455 SER Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 523 VAL Chi-restraints excluded: chain 2 residue 556 VAL Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 833 ASP Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 167 SER Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 221 LEU Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 502 ILE Chi-restraints excluded: chain 3 residue 533 ILE Chi-restraints excluded: chain 3 residue 535 LEU Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 458 LYS Chi-restraints excluded: chain 4 residue 485 LEU Chi-restraints excluded: chain 4 residue 492 HIS Chi-restraints excluded: chain 4 residue 564 ILE Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 605 ILE Chi-restraints excluded: chain 4 residue 616 LEU Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 4 residue 728 TYR Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 218 GLU Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 444 SER Chi-restraints excluded: chain 5 residue 485 MET Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 575 ILE Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 594 ILE Chi-restraints excluded: chain 5 residue 632 GLN Chi-restraints excluded: chain 5 residue 648 ILE Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 646 ILE Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 700 ASN Chi-restraints excluded: chain 6 residue 742 ILE Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 117 PHE Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 279 THR Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 393 LEU Chi-restraints excluded: chain 7 residue 416 LYS Chi-restraints excluded: chain 7 residue 433 LEU Chi-restraints excluded: chain 7 residue 464 VAL Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 476 ILE Chi-restraints excluded: chain 7 residue 497 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 601 LEU Chi-restraints excluded: chain 7 residue 642 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 728 TYR Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 803 ARG Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 576 HIS Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 598 THR Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 464 VAL Chi-restraints excluded: chain F residue 473 ILE Chi-restraints excluded: chain F residue 476 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 601 LEU Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain F residue 712 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 619 optimal weight: 8.9990 chunk 422 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 554 optimal weight: 0.3980 chunk 307 optimal weight: 2.9990 chunk 635 optimal weight: 0.0370 chunk 514 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 380 optimal weight: 5.9990 chunk 668 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 51 ASN ** 4 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 651 GLN 6 669 HIS 6 700 ASN 7 544 GLN 7 622 HIS B 51 ASN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN D 576 HIS E 669 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 63714 Z= 0.182 Angle : 0.702 11.719 86712 Z= 0.359 Chirality : 0.044 0.273 10082 Planarity : 0.004 0.063 10746 Dihedral : 14.524 131.365 9770 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 4.09 % Allowed : 17.16 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.09), residues: 7548 helix: 0.56 (0.10), residues: 2670 sheet: -1.94 (0.16), residues: 1068 loop : -2.64 (0.09), residues: 3810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.013 0.001 HIS D 576 PHE 0.026 0.001 PHE D 31 TYR 0.020 0.001 TYR B 327 ARG 0.011 0.000 ARG 5 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 760 time to evaluate : 5.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 279 THR cc_start: 0.8003 (m) cc_final: 0.7781 (p) REVERT: 2 302 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7746 (t) REVERT: 2 781 MET cc_start: 0.7413 (mtt) cc_final: 0.7136 (ptt) REVERT: 3 97 ILE cc_start: 0.9128 (mt) cc_final: 0.8903 (mm) REVERT: 3 117 GLU cc_start: 0.8481 (pt0) cc_final: 0.8247 (pt0) REVERT: 3 234 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6981 (mm-30) REVERT: 3 261 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7614 (ptp) REVERT: 3 264 MET cc_start: 0.8013 (mtt) cc_final: 0.7168 (mtt) REVERT: 3 279 ASP cc_start: 0.7735 (m-30) cc_final: 0.7332 (m-30) REVERT: 3 325 THR cc_start: 0.9334 (OUTLIER) cc_final: 0.9099 (m) REVERT: 3 346 ASP cc_start: 0.7364 (m-30) cc_final: 0.6936 (m-30) REVERT: 3 407 MET cc_start: 0.7840 (mtp) cc_final: 0.7554 (mtp) REVERT: 3 490 MET cc_start: 0.8560 (tpp) cc_final: 0.8291 (tpp) REVERT: 3 535 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8503 (pp) REVERT: 4 206 ARG cc_start: 0.8741 (mmt90) cc_final: 0.8475 (mpt180) REVERT: 4 229 GLN cc_start: 0.7710 (mt0) cc_final: 0.7468 (tm-30) REVERT: 4 273 ASP cc_start: 0.8435 (m-30) cc_final: 0.8115 (m-30) REVERT: 4 370 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7735 (ptm-80) REVERT: 4 533 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7274 (pt) REVERT: 4 561 ASP cc_start: 0.6776 (t0) cc_final: 0.6504 (p0) REVERT: 4 702 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8448 (m-10) REVERT: 4 780 MET cc_start: 0.7392 (mmp) cc_final: 0.6976 (mmm) REVERT: 5 65 MET cc_start: 0.7842 (ttp) cc_final: 0.7124 (mtp) REVERT: 5 76 TYR cc_start: 0.8170 (t80) cc_final: 0.7580 (t80) REVERT: 5 234 LYS cc_start: 0.6732 (pptt) cc_final: 0.6269 (ptpt) REVERT: 5 404 MET cc_start: 0.8253 (ppp) cc_final: 0.8039 (ppp) REVERT: 5 449 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7874 (tt) REVERT: 5 465 GLU cc_start: 0.8003 (tp30) cc_final: 0.7471 (tp30) REVERT: 5 469 MET cc_start: 0.8868 (mmt) cc_final: 0.8629 (mmt) REVERT: 5 513 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8447 (pp) REVERT: 5 689 MET cc_start: 0.8710 (mmm) cc_final: 0.8113 (mtt) REVERT: 6 175 TYR cc_start: 0.8469 (t80) cc_final: 0.8132 (t80) REVERT: 6 261 ARG cc_start: 0.3512 (mpt180) cc_final: 0.2725 (mtt90) REVERT: 6 379 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8691 (m) REVERT: 6 525 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8119 (pt) REVERT: 6 646 ILE cc_start: 0.6594 (OUTLIER) cc_final: 0.6081 (mm) REVERT: 7 84 ASP cc_start: 0.7821 (m-30) cc_final: 0.7494 (m-30) REVERT: 7 298 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8963 (pp) REVERT: 7 393 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6805 (tt) REVERT: 7 394 THR cc_start: 0.6818 (OUTLIER) cc_final: 0.6338 (m) REVERT: 7 402 MET cc_start: 0.8394 (tpp) cc_final: 0.8020 (tpp) REVERT: 7 509 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7955 (mm-30) REVERT: 7 529 MET cc_start: 0.8479 (mmt) cc_final: 0.8197 (mmt) REVERT: 7 609 ASP cc_start: 0.8156 (m-30) cc_final: 0.7943 (m-30) REVERT: 7 675 MET cc_start: 0.5842 (mtt) cc_final: 0.5463 (ttt) REVERT: A 279 THR cc_start: 0.8015 (m) cc_final: 0.7784 (p) REVERT: A 302 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7657 (t) REVERT: A 622 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7726 (tp30) REVERT: B 234 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6767 (mm-30) REVERT: B 279 ASP cc_start: 0.7701 (m-30) cc_final: 0.7338 (m-30) REVERT: B 346 ASP cc_start: 0.7293 (m-30) cc_final: 0.6962 (m-30) REVERT: B 490 MET cc_start: 0.8846 (tpp) cc_final: 0.8508 (tpp) REVERT: B 522 GLN cc_start: 0.8194 (mp10) cc_final: 0.7490 (tm-30) REVERT: C 229 GLN cc_start: 0.7668 (mt0) cc_final: 0.7429 (tm-30) REVERT: C 273 ASP cc_start: 0.8455 (m-30) cc_final: 0.8170 (m-30) REVERT: C 382 MET cc_start: 0.8603 (tpp) cc_final: 0.8180 (mmt) REVERT: C 561 ASP cc_start: 0.6897 (t0) cc_final: 0.6394 (p0) REVERT: C 728 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7352 (t80) REVERT: C 780 MET cc_start: 0.7381 (mmp) cc_final: 0.6836 (mmm) REVERT: C 803 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6989 (ptp-170) REVERT: D 65 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.6897 (mtp) REVERT: D 76 TYR cc_start: 0.8035 (t80) cc_final: 0.7340 (t80) REVERT: D 234 LYS cc_start: 0.6753 (pptt) cc_final: 0.6144 (ptpt) REVERT: D 329 LYS cc_start: 0.8660 (tptp) cc_final: 0.8302 (mtmm) REVERT: D 458 MET cc_start: 0.7296 (ptp) cc_final: 0.6889 (ppp) REVERT: D 465 GLU cc_start: 0.8000 (tp30) cc_final: 0.7753 (tp30) REVERT: D 469 MET cc_start: 0.8947 (mmt) cc_final: 0.8705 (mmt) REVERT: D 513 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8655 (pp) REVERT: D 689 MET cc_start: 0.8580 (mmm) cc_final: 0.8193 (mtt) REVERT: E 175 TYR cc_start: 0.8353 (t80) cc_final: 0.8014 (t80) REVERT: E 261 ARG cc_start: 0.4078 (mpt180) cc_final: 0.3234 (mtt90) REVERT: E 379 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8660 (m) REVERT: E 387 GLU cc_start: 0.8546 (tp30) cc_final: 0.8276 (tp30) REVERT: E 527 ASP cc_start: 0.8584 (t0) cc_final: 0.8264 (t70) REVERT: E 636 CYS cc_start: 0.8463 (t) cc_final: 0.8240 (p) REVERT: E 646 ILE cc_start: 0.6037 (OUTLIER) cc_final: 0.5710 (mm) REVERT: F 84 ASP cc_start: 0.7621 (m-30) cc_final: 0.7265 (m-30) REVERT: F 298 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8925 (pp) REVERT: F 393 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7042 (tt) REVERT: F 394 THR cc_start: 0.6725 (OUTLIER) cc_final: 0.6327 (m) REVERT: F 442 LYS cc_start: 0.7134 (tptt) cc_final: 0.6599 (tttt) REVERT: F 541 MET cc_start: 0.8169 (mmt) cc_final: 0.7864 (mmt) REVERT: F 675 MET cc_start: 0.5867 (mtt) cc_final: 0.5584 (ttt) outliers start: 270 outliers final: 170 residues processed: 964 average time/residue: 0.5599 time to fit residues: 948.8610 Evaluate side-chains 910 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 715 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 205 ARG Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 306 LEU Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 523 VAL Chi-restraints excluded: chain 2 residue 556 VAL Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 806 THR Chi-restraints excluded: chain 2 residue 833 ASP Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 167 SER Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 221 LEU Chi-restraints excluded: chain 3 residue 233 THR Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 502 ILE Chi-restraints excluded: chain 3 residue 533 ILE Chi-restraints excluded: chain 3 residue 535 LEU Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 370 ARG Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 451 ARG Chi-restraints excluded: chain 4 residue 456 LEU Chi-restraints excluded: chain 4 residue 458 LYS Chi-restraints excluded: chain 4 residue 474 LEU Chi-restraints excluded: chain 4 residue 492 HIS Chi-restraints excluded: chain 4 residue 533 LEU Chi-restraints excluded: chain 4 residue 564 ILE Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 616 LEU Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 4 residue 756 GLU Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 236 CYS Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 377 SER Chi-restraints excluded: chain 5 residue 444 SER Chi-restraints excluded: chain 5 residue 449 LEU Chi-restraints excluded: chain 5 residue 485 MET Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 575 ILE Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 594 ILE Chi-restraints excluded: chain 5 residue 648 ILE Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 457 CYS Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 646 ILE Chi-restraints excluded: chain 6 residue 700 ASN Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 83 ASP Chi-restraints excluded: chain 7 residue 117 PHE Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 269 VAL Chi-restraints excluded: chain 7 residue 279 THR Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 393 LEU Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 416 LYS Chi-restraints excluded: chain 7 residue 433 LEU Chi-restraints excluded: chain 7 residue 464 VAL Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 476 ILE Chi-restraints excluded: chain 7 residue 497 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 601 LEU Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 728 TYR Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 803 ARG Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 598 THR Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 819 ILE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 464 VAL Chi-restraints excluded: chain F residue 473 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 601 LEU Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain F residue 696 SER Chi-restraints excluded: chain F residue 712 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 250 optimal weight: 10.0000 chunk 670 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 436 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 745 optimal weight: 10.0000 chunk 618 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 391 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 856 GLN 3 51 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 354 HIS 4 651 GLN 6 669 HIS 6 700 ASN 7 68 GLN B 51 ASN B 330 HIS B 351 ASN B 554 ASN C 651 GLN C 808 HIS D 253 GLN E 669 HIS ** E 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 544 GLN F 622 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 63714 Z= 0.322 Angle : 0.780 14.111 86712 Z= 0.399 Chirality : 0.047 0.310 10082 Planarity : 0.005 0.064 10746 Dihedral : 14.595 132.515 9768 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 4.66 % Allowed : 17.27 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.41 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.09), residues: 7548 helix: 0.64 (0.10), residues: 2658 sheet: -1.86 (0.16), residues: 1048 loop : -2.71 (0.09), residues: 3842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 111 HIS 0.010 0.001 HIS 3 530 PHE 0.021 0.002 PHE 4 439 TYR 0.020 0.002 TYR 6 777 ARG 0.012 0.001 ARG 5 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 727 time to evaluate : 6.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 302 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7629 (t) REVERT: 2 614 ASP cc_start: 0.8227 (p0) cc_final: 0.7447 (t0) REVERT: 2 781 MET cc_start: 0.7453 (mtt) cc_final: 0.7175 (ptt) REVERT: 3 97 ILE cc_start: 0.9243 (mt) cc_final: 0.8926 (pt) REVERT: 3 117 GLU cc_start: 0.8638 (pt0) cc_final: 0.8320 (pt0) REVERT: 3 234 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7220 (mm-30) REVERT: 3 279 ASP cc_start: 0.7792 (m-30) cc_final: 0.7399 (m-30) REVERT: 3 325 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9083 (m) REVERT: 3 346 ASP cc_start: 0.7388 (m-30) cc_final: 0.6964 (m-30) REVERT: 3 407 MET cc_start: 0.8053 (mtp) cc_final: 0.7766 (mtp) REVERT: 3 482 ASP cc_start: 0.8072 (p0) cc_final: 0.7487 (t0) REVERT: 3 490 MET cc_start: 0.8634 (tpp) cc_final: 0.8375 (tpp) REVERT: 3 535 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8556 (pp) REVERT: 4 206 ARG cc_start: 0.8763 (mmt90) cc_final: 0.8535 (mpt180) REVERT: 4 273 ASP cc_start: 0.8518 (m-30) cc_final: 0.8194 (m-30) REVERT: 4 370 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7879 (ptm-80) REVERT: 4 533 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7328 (pt) REVERT: 4 561 ASP cc_start: 0.6877 (t0) cc_final: 0.6489 (p0) REVERT: 4 702 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8335 (m-10) REVERT: 4 780 MET cc_start: 0.7579 (mmp) cc_final: 0.7092 (mmm) REVERT: 5 65 MET cc_start: 0.8034 (ttp) cc_final: 0.7278 (mtp) REVERT: 5 76 TYR cc_start: 0.8370 (t80) cc_final: 0.7714 (t80) REVERT: 5 234 LYS cc_start: 0.6839 (pptt) cc_final: 0.6236 (ptpt) REVERT: 5 331 LEU cc_start: 0.7926 (pt) cc_final: 0.7687 (pp) REVERT: 5 404 MET cc_start: 0.8255 (ppp) cc_final: 0.8027 (ppp) REVERT: 5 449 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7991 (tt) REVERT: 5 465 GLU cc_start: 0.8119 (tp30) cc_final: 0.7523 (tp30) REVERT: 5 469 MET cc_start: 0.8842 (mmt) cc_final: 0.8593 (mmt) REVERT: 5 513 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8593 (pp) REVERT: 5 689 MET cc_start: 0.8705 (mmm) cc_final: 0.8204 (mtt) REVERT: 6 175 TYR cc_start: 0.8639 (t80) cc_final: 0.8350 (t80) REVERT: 6 379 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8709 (m) REVERT: 6 525 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8284 (pt) REVERT: 6 777 TYR cc_start: 0.7658 (t80) cc_final: 0.7329 (t80) REVERT: 7 298 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9042 (pp) REVERT: 7 394 THR cc_start: 0.6950 (OUTLIER) cc_final: 0.6651 (m) REVERT: 7 499 LYS cc_start: 0.8545 (tppt) cc_final: 0.8210 (tppt) REVERT: 7 529 MET cc_start: 0.8444 (mmt) cc_final: 0.8072 (mmt) REVERT: 7 609 ASP cc_start: 0.8178 (m-30) cc_final: 0.7933 (m-30) REVERT: 7 675 MET cc_start: 0.5893 (mtt) cc_final: 0.5511 (ttt) REVERT: 7 717 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9367 (mm) REVERT: A 279 THR cc_start: 0.8077 (m) cc_final: 0.7867 (p) REVERT: A 302 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7533 (t) REVERT: B 234 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7092 (mm-30) REVERT: B 279 ASP cc_start: 0.7820 (m-30) cc_final: 0.7427 (m-30) REVERT: B 346 ASP cc_start: 0.7376 (m-30) cc_final: 0.7030 (m-30) REVERT: B 482 ASP cc_start: 0.8191 (p0) cc_final: 0.7529 (m-30) REVERT: C 229 GLN cc_start: 0.7784 (mt0) cc_final: 0.7567 (tm-30) REVERT: C 273 ASP cc_start: 0.8594 (m-30) cc_final: 0.8274 (m-30) REVERT: C 561 ASP cc_start: 0.6897 (t0) cc_final: 0.6116 (p0) REVERT: C 702 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8530 (m-10) REVERT: C 780 MET cc_start: 0.7516 (mmp) cc_final: 0.6953 (mmm) REVERT: C 803 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7314 (mtp180) REVERT: D 65 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7216 (mtp) REVERT: D 76 TYR cc_start: 0.8254 (t80) cc_final: 0.7558 (t80) REVERT: D 234 LYS cc_start: 0.6552 (pptt) cc_final: 0.6020 (ptpt) REVERT: D 458 MET cc_start: 0.7201 (ptp) cc_final: 0.6483 (ppp) REVERT: D 465 GLU cc_start: 0.8141 (tp30) cc_final: 0.7714 (tp30) REVERT: D 469 MET cc_start: 0.8964 (mmt) cc_final: 0.8673 (mmt) REVERT: D 513 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8709 (pp) REVERT: D 689 MET cc_start: 0.8541 (mmm) cc_final: 0.8049 (mtt) REVERT: E 175 TYR cc_start: 0.8557 (t80) cc_final: 0.8280 (t80) REVERT: E 261 ARG cc_start: 0.4200 (mpt180) cc_final: 0.3663 (mtt90) REVERT: E 379 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8670 (m) REVERT: F 298 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9013 (pp) REVERT: F 394 THR cc_start: 0.6861 (OUTLIER) cc_final: 0.6545 (m) REVERT: F 442 LYS cc_start: 0.7250 (tptt) cc_final: 0.6701 (ttmt) REVERT: F 529 MET cc_start: 0.8464 (mmt) cc_final: 0.7887 (mmt) REVERT: F 541 MET cc_start: 0.8376 (mmt) cc_final: 0.8120 (mmt) REVERT: F 675 MET cc_start: 0.5806 (mtt) cc_final: 0.5501 (ttt) outliers start: 308 outliers final: 209 residues processed: 956 average time/residue: 0.5497 time to fit residues: 920.0434 Evaluate side-chains 913 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 683 time to evaluate : 5.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 205 ARG Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 306 LEU Chi-restraints excluded: chain 2 residue 314 LEU Chi-restraints excluded: chain 2 residue 347 ILE Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 455 SER Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 523 VAL Chi-restraints excluded: chain 2 residue 552 ILE Chi-restraints excluded: chain 2 residue 597 VAL Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 675 SER Chi-restraints excluded: chain 2 residue 806 THR Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 129 LEU Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 221 LEU Chi-restraints excluded: chain 3 residue 233 THR Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 502 ILE Chi-restraints excluded: chain 3 residue 533 ILE Chi-restraints excluded: chain 3 residue 535 LEU Chi-restraints excluded: chain 3 residue 561 ILE Chi-restraints excluded: chain 4 residue 198 LEU Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 370 ARG Chi-restraints excluded: chain 4 residue 389 CYS Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 433 ILE Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 451 ARG Chi-restraints excluded: chain 4 residue 458 LYS Chi-restraints excluded: chain 4 residue 474 LEU Chi-restraints excluded: chain 4 residue 492 HIS Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 533 LEU Chi-restraints excluded: chain 4 residue 551 THR Chi-restraints excluded: chain 4 residue 564 ILE Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 4 residue 756 GLU Chi-restraints excluded: chain 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 27 ILE Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 236 CYS Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 349 PHE Chi-restraints excluded: chain 5 residue 377 SER Chi-restraints excluded: chain 5 residue 410 ILE Chi-restraints excluded: chain 5 residue 444 SER Chi-restraints excluded: chain 5 residue 449 LEU Chi-restraints excluded: chain 5 residue 478 CYS Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 575 ILE Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 594 ILE Chi-restraints excluded: chain 5 residue 648 ILE Chi-restraints excluded: chain 6 residue 106 VAL Chi-restraints excluded: chain 6 residue 118 PHE Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 348 VAL Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 457 CYS Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 572 CYS Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 609 THR Chi-restraints excluded: chain 6 residue 613 VAL Chi-restraints excluded: chain 6 residue 695 LEU Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 742 ILE Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 83 ASP Chi-restraints excluded: chain 7 residue 158 THR Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 258 ILE Chi-restraints excluded: chain 7 residue 269 VAL Chi-restraints excluded: chain 7 residue 279 THR Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 416 LYS Chi-restraints excluded: chain 7 residue 459 MET Chi-restraints excluded: chain 7 residue 464 VAL Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 497 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 590 LEU Chi-restraints excluded: chain 7 residue 601 LEU Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain 7 residue 717 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 702 PHE Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain C residue 803 ARG Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 349 PHE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 CYS Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 637 GLU Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 598 THR Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 742 ILE Chi-restraints excluded: chain E residue 751 LEU Chi-restraints excluded: chain E residue 796 THR Chi-restraints excluded: chain E residue 819 ILE Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 464 VAL Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 601 LEU Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain F residue 696 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 718 optimal weight: 0.0030 chunk 83 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 chunk 544 optimal weight: 8.9990 chunk 421 optimal weight: 9.9990 chunk 627 optimal weight: 7.9990 chunk 416 optimal weight: 4.9990 chunk 742 optimal weight: 3.9990 chunk 464 optimal weight: 10.0000 chunk 452 optimal weight: 4.9990 chunk 342 optimal weight: 1.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 856 GLN 3 51 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 410 GLN 6 669 HIS 6 700 ASN 6 730 HIS A 202 ASN B 51 ASN E 669 HIS E 690 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 63714 Z= 0.239 Angle : 0.740 13.938 86712 Z= 0.377 Chirality : 0.045 0.291 10082 Planarity : 0.005 0.065 10746 Dihedral : 14.478 129.837 9766 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 3.93 % Allowed : 18.57 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.41 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.10), residues: 7548 helix: 0.76 (0.10), residues: 2668 sheet: -1.81 (0.16), residues: 1048 loop : -2.65 (0.09), residues: 3832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.007 0.001 HIS 3 530 PHE 0.014 0.001 PHE C 439 TYR 0.022 0.001 TYR B 372 ARG 0.013 0.000 ARG 5 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 712 time to evaluate : 5.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 255 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8384 (tt) REVERT: 2 302 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7556 (t) REVERT: 2 614 ASP cc_start: 0.8163 (p0) cc_final: 0.7383 (t0) REVERT: 3 97 ILE cc_start: 0.9208 (mt) cc_final: 0.8892 (pt) REVERT: 3 117 GLU cc_start: 0.8587 (pt0) cc_final: 0.8252 (pt0) REVERT: 3 234 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7157 (mm-30) REVERT: 3 261 MET cc_start: 0.8118 (ttp) cc_final: 0.7577 (ptp) REVERT: 3 264 MET cc_start: 0.7938 (mtt) cc_final: 0.7378 (mtt) REVERT: 3 279 ASP cc_start: 0.7731 (m-30) cc_final: 0.7288 (m-30) REVERT: 3 325 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.9116 (m) REVERT: 3 346 ASP cc_start: 0.7371 (m-30) cc_final: 0.6945 (m-30) REVERT: 3 482 ASP cc_start: 0.8155 (p0) cc_final: 0.7316 (t0) REVERT: 3 490 MET cc_start: 0.8634 (tpp) cc_final: 0.8370 (tpp) REVERT: 3 535 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8531 (pp) REVERT: 4 206 ARG cc_start: 0.8766 (mmt90) cc_final: 0.8525 (mpt180) REVERT: 4 273 ASP cc_start: 0.8458 (m-30) cc_final: 0.8128 (m-30) REVERT: 4 370 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7927 (ptm-80) REVERT: 4 533 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7337 (pt) REVERT: 4 561 ASP cc_start: 0.6845 (t0) cc_final: 0.6449 (p0) REVERT: 4 702 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8350 (m-10) REVERT: 4 780 MET cc_start: 0.7571 (mmp) cc_final: 0.7092 (mmm) REVERT: 5 65 MET cc_start: 0.8049 (ttp) cc_final: 0.7216 (mtp) REVERT: 5 76 TYR cc_start: 0.8333 (t80) cc_final: 0.7585 (t80) REVERT: 5 234 LYS cc_start: 0.6537 (pptt) cc_final: 0.5909 (ptpt) REVERT: 5 404 MET cc_start: 0.8249 (ppp) cc_final: 0.7961 (ppp) REVERT: 5 449 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7937 (tt) REVERT: 5 465 GLU cc_start: 0.7990 (tp30) cc_final: 0.7625 (tp30) REVERT: 5 469 MET cc_start: 0.8879 (mmt) cc_final: 0.8637 (mmt) REVERT: 5 513 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8534 (pp) REVERT: 5 689 MET cc_start: 0.8651 (mmm) cc_final: 0.8116 (mtt) REVERT: 6 175 TYR cc_start: 0.8555 (t80) cc_final: 0.8217 (t80) REVERT: 6 379 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8716 (m) REVERT: 6 540 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.6670 (p90) REVERT: 6 777 TYR cc_start: 0.7674 (t80) cc_final: 0.7229 (t80) REVERT: 7 298 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9023 (pp) REVERT: 7 394 THR cc_start: 0.6656 (OUTLIER) cc_final: 0.6390 (m) REVERT: 7 402 MET cc_start: 0.8295 (tpp) cc_final: 0.7780 (tpp) REVERT: 7 443 ARG cc_start: 0.7992 (tmm-80) cc_final: 0.7449 (tmm-80) REVERT: 7 529 MET cc_start: 0.8427 (mmt) cc_final: 0.8055 (mmt) REVERT: 7 609 ASP cc_start: 0.8194 (m-30) cc_final: 0.7985 (m-30) REVERT: 7 675 MET cc_start: 0.5929 (mtt) cc_final: 0.5496 (ttt) REVERT: 7 717 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9361 (mm) REVERT: A 279 THR cc_start: 0.8043 (m) cc_final: 0.7828 (p) REVERT: A 302 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7474 (t) REVERT: A 781 MET cc_start: 0.7794 (mtt) cc_final: 0.7160 (ptt) REVERT: B 205 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7317 (tppt) REVERT: B 234 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7090 (mm-30) REVERT: B 279 ASP cc_start: 0.7792 (m-30) cc_final: 0.7376 (m-30) REVERT: B 346 ASP cc_start: 0.7486 (m-30) cc_final: 0.7087 (m-30) REVERT: B 482 ASP cc_start: 0.8193 (p0) cc_final: 0.7473 (m-30) REVERT: B 490 MET cc_start: 0.8890 (tpp) cc_final: 0.8569 (tpp) REVERT: C 273 ASP cc_start: 0.8562 (m-30) cc_final: 0.8244 (m-30) REVERT: C 561 ASP cc_start: 0.6898 (t0) cc_final: 0.6416 (p0) REVERT: C 702 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8486 (m-10) REVERT: C 780 MET cc_start: 0.7507 (mmp) cc_final: 0.6950 (mmm) REVERT: D 65 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7100 (mtp) REVERT: D 76 TYR cc_start: 0.8224 (t80) cc_final: 0.7454 (t80) REVERT: D 234 LYS cc_start: 0.6528 (pptt) cc_final: 0.6023 (ptpt) REVERT: D 260 GLU cc_start: 0.8070 (tp30) cc_final: 0.7763 (tp30) REVERT: D 449 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7718 (tt) REVERT: D 458 MET cc_start: 0.7044 (ptp) cc_final: 0.6570 (ppp) REVERT: D 465 GLU cc_start: 0.7980 (tp30) cc_final: 0.7655 (mm-30) REVERT: D 469 MET cc_start: 0.9027 (mmt) cc_final: 0.8766 (mmt) REVERT: D 481 GLU cc_start: 0.8500 (tp30) cc_final: 0.8296 (tp30) REVERT: D 513 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8594 (pp) REVERT: D 676 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7640 (t-170) REVERT: D 689 MET cc_start: 0.8511 (mmm) cc_final: 0.8006 (mtt) REVERT: E 175 TYR cc_start: 0.8480 (t80) cc_final: 0.8160 (t80) REVERT: E 261 ARG cc_start: 0.4254 (mpt180) cc_final: 0.3668 (mtt90) REVERT: E 379 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8695 (m) REVERT: E 646 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5820 (mm) REVERT: F 247 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7419 (ttm-80) REVERT: F 298 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8983 (pp) REVERT: F 393 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7247 (tt) REVERT: F 394 THR cc_start: 0.6839 (OUTLIER) cc_final: 0.6455 (m) REVERT: F 541 MET cc_start: 0.8362 (mmt) cc_final: 0.8091 (mmt) REVERT: F 675 MET cc_start: 0.5812 (mtt) cc_final: 0.5493 (ttt) outliers start: 260 outliers final: 186 residues processed: 915 average time/residue: 0.5352 time to fit residues: 858.3906 Evaluate side-chains 886 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 675 time to evaluate : 5.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 306 LEU Chi-restraints excluded: chain 2 residue 314 LEU Chi-restraints excluded: chain 2 residue 347 ILE Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 455 SER Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 523 VAL Chi-restraints excluded: chain 2 residue 597 VAL Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 675 SER Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 129 LEU Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 233 THR Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 502 ILE Chi-restraints excluded: chain 3 residue 533 ILE Chi-restraints excluded: chain 3 residue 535 LEU Chi-restraints excluded: chain 4 residue 224 LEU Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 370 ARG Chi-restraints excluded: chain 4 residue 389 CYS Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 433 ILE Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 451 ARG Chi-restraints excluded: chain 4 residue 458 LYS Chi-restraints excluded: chain 4 residue 492 HIS Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 533 LEU Chi-restraints excluded: chain 4 residue 564 ILE Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 616 LEU Chi-restraints excluded: chain 4 residue 634 PHE Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 4 residue 756 GLU Chi-restraints excluded: chain 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 181 ILE Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 236 CYS Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 377 SER Chi-restraints excluded: chain 5 residue 389 VAL Chi-restraints excluded: chain 5 residue 405 ARG Chi-restraints excluded: chain 5 residue 444 SER Chi-restraints excluded: chain 5 residue 449 LEU Chi-restraints excluded: chain 5 residue 485 MET Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 575 ILE Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 594 ILE Chi-restraints excluded: chain 5 residue 648 ILE Chi-restraints excluded: chain 6 residue 106 VAL Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 348 VAL Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 457 CYS Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 540 HIS Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 572 CYS Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 641 PHE Chi-restraints excluded: chain 6 residue 695 LEU Chi-restraints excluded: chain 6 residue 742 ILE Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 83 ASP Chi-restraints excluded: chain 7 residue 117 PHE Chi-restraints excluded: chain 7 residue 158 THR Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 269 VAL Chi-restraints excluded: chain 7 residue 279 THR Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 416 LYS Chi-restraints excluded: chain 7 residue 459 MET Chi-restraints excluded: chain 7 residue 464 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 491 VAL Chi-restraints excluded: chain 7 residue 497 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 601 LEU Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain 7 residue 717 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 702 PHE Chi-restraints excluded: chain C residue 746 PHE Chi-restraints excluded: chain C residue 756 GLU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 CYS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 598 THR Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 796 THR Chi-restraints excluded: chain E residue 797 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 464 VAL Chi-restraints excluded: chain F residue 473 ILE Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 601 LEU Chi-restraints excluded: chain F residue 696 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 459 optimal weight: 6.9990 chunk 296 optimal weight: 5.9990 chunk 443 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 471 optimal weight: 1.9990 chunk 505 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 583 optimal weight: 0.0980 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 202 ASN 3 51 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS B 51 ASN C 410 GLN C 413 HIS E 669 HIS F 554 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 63714 Z= 0.197 Angle : 0.729 14.689 86712 Z= 0.368 Chirality : 0.045 0.278 10082 Planarity : 0.004 0.066 10746 Dihedral : 14.352 129.826 9766 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.99 % Favored : 89.98 % Rotamer: Outliers : 3.63 % Allowed : 19.16 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.41 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.10), residues: 7548 helix: 0.91 (0.10), residues: 2654 sheet: -1.67 (0.16), residues: 1064 loop : -2.61 (0.09), residues: 3830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.006 0.001 HIS 3 530 PHE 0.016 0.001 PHE 5 31 TYR 0.016 0.001 TYR 3 211 ARG 0.014 0.000 ARG 5 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 719 time to evaluate : 5.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 255 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8384 (tt) REVERT: 2 302 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7537 (t) REVERT: 2 614 ASP cc_start: 0.8168 (p0) cc_final: 0.7363 (t0) REVERT: 3 97 ILE cc_start: 0.9124 (mt) cc_final: 0.8862 (pt) REVERT: 3 117 GLU cc_start: 0.8580 (pt0) cc_final: 0.8286 (pt0) REVERT: 3 205 LYS cc_start: 0.7559 (mmmt) cc_final: 0.7163 (tppt) REVERT: 3 234 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7137 (mm-30) REVERT: 3 261 MET cc_start: 0.8107 (ttp) cc_final: 0.7629 (ptp) REVERT: 3 264 MET cc_start: 0.7989 (mtt) cc_final: 0.7358 (mtt) REVERT: 3 279 ASP cc_start: 0.7704 (m-30) cc_final: 0.7245 (m-30) REVERT: 3 325 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9098 (m) REVERT: 3 346 ASP cc_start: 0.7352 (m-30) cc_final: 0.6934 (m-30) REVERT: 3 482 ASP cc_start: 0.8152 (p0) cc_final: 0.7226 (t0) REVERT: 3 490 MET cc_start: 0.8648 (tpp) cc_final: 0.8384 (tpp) REVERT: 3 535 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8506 (pp) REVERT: 4 194 PHE cc_start: 0.8701 (t80) cc_final: 0.8333 (t80) REVERT: 4 206 ARG cc_start: 0.8745 (mmt90) cc_final: 0.8496 (mpt180) REVERT: 4 273 ASP cc_start: 0.8430 (m-30) cc_final: 0.8106 (m-30) REVERT: 4 370 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7900 (ptm-80) REVERT: 4 533 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7266 (pt) REVERT: 4 561 ASP cc_start: 0.6762 (t0) cc_final: 0.6365 (p0) REVERT: 4 702 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8311 (m-10) REVERT: 4 780 MET cc_start: 0.7534 (mmp) cc_final: 0.7084 (mmm) REVERT: 5 65 MET cc_start: 0.8046 (ttp) cc_final: 0.7168 (mtp) REVERT: 5 76 TYR cc_start: 0.8330 (t80) cc_final: 0.7541 (t80) REVERT: 5 234 LYS cc_start: 0.6703 (pptt) cc_final: 0.6069 (ptpt) REVERT: 5 404 MET cc_start: 0.8308 (ppp) cc_final: 0.8031 (ppp) REVERT: 5 449 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7907 (tt) REVERT: 5 465 GLU cc_start: 0.7873 (tp30) cc_final: 0.7562 (tp30) REVERT: 5 469 MET cc_start: 0.8877 (mmt) cc_final: 0.8659 (mmt) REVERT: 5 513 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8484 (pp) REVERT: 5 676 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7290 (t-170) REVERT: 5 689 MET cc_start: 0.8649 (mmm) cc_final: 0.8106 (mtt) REVERT: 6 175 TYR cc_start: 0.8511 (t80) cc_final: 0.8179 (t80) REVERT: 6 379 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8710 (m) REVERT: 6 540 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6649 (p90) REVERT: 6 646 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6306 (mm) REVERT: 6 777 TYR cc_start: 0.7453 (t80) cc_final: 0.7213 (t80) REVERT: 7 298 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9002 (pp) REVERT: 7 394 THR cc_start: 0.6698 (OUTLIER) cc_final: 0.6393 (m) REVERT: 7 443 ARG cc_start: 0.7858 (tmm-80) cc_final: 0.7344 (tmm-80) REVERT: 7 529 MET cc_start: 0.8522 (mmt) cc_final: 0.8125 (mmt) REVERT: 7 675 MET cc_start: 0.5920 (mtt) cc_final: 0.5301 (tpt) REVERT: A 255 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 302 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7480 (t) REVERT: A 781 MET cc_start: 0.7766 (mtt) cc_final: 0.7191 (ptt) REVERT: B 205 LYS cc_start: 0.7464 (mmmt) cc_final: 0.7240 (tppt) REVERT: B 234 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 279 ASP cc_start: 0.7714 (m-30) cc_final: 0.7287 (m-30) REVERT: B 346 ASP cc_start: 0.7401 (m-30) cc_final: 0.7054 (m-30) REVERT: B 482 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: B 490 MET cc_start: 0.8897 (tpp) cc_final: 0.8656 (tpp) REVERT: C 273 ASP cc_start: 0.8522 (m-30) cc_final: 0.8213 (m-30) REVERT: C 561 ASP cc_start: 0.6926 (t0) cc_final: 0.6439 (p0) REVERT: C 702 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8423 (m-10) REVERT: C 780 MET cc_start: 0.7397 (mmp) cc_final: 0.6866 (mmm) REVERT: D 65 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7193 (mtp) REVERT: D 76 TYR cc_start: 0.8185 (t80) cc_final: 0.7447 (t80) REVERT: D 234 LYS cc_start: 0.6618 (pptt) cc_final: 0.5979 (ptpt) REVERT: D 260 GLU cc_start: 0.8118 (tp30) cc_final: 0.7896 (tp30) REVERT: D 465 GLU cc_start: 0.7895 (tp30) cc_final: 0.7635 (mm-30) REVERT: D 469 MET cc_start: 0.9026 (mmt) cc_final: 0.8769 (mmt) REVERT: D 513 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8551 (pp) REVERT: D 689 MET cc_start: 0.8510 (mmm) cc_final: 0.7968 (mtt) REVERT: E 175 TYR cc_start: 0.8411 (t80) cc_final: 0.8101 (t80) REVERT: E 261 ARG cc_start: 0.4107 (mpt180) cc_final: 0.3614 (mtt90) REVERT: E 379 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8679 (m) REVERT: E 527 ASP cc_start: 0.8589 (t0) cc_final: 0.8288 (t70) REVERT: E 646 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5846 (mm) REVERT: F 247 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.7274 (ttm-80) REVERT: F 298 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8965 (pp) REVERT: F 393 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7080 (tt) REVERT: F 394 THR cc_start: 0.6720 (OUTLIER) cc_final: 0.6340 (m) REVERT: F 541 MET cc_start: 0.8311 (mmt) cc_final: 0.8062 (mmt) REVERT: F 675 MET cc_start: 0.5761 (mtt) cc_final: 0.5477 (ttt) outliers start: 240 outliers final: 169 residues processed: 901 average time/residue: 0.5307 time to fit residues: 843.0809 Evaluate side-chains 866 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 671 time to evaluate : 5.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 306 LEU Chi-restraints excluded: chain 2 residue 314 LEU Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 455 SER Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 523 VAL Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 806 THR Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 129 LEU Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 233 THR Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 502 ILE Chi-restraints excluded: chain 3 residue 533 ILE Chi-restraints excluded: chain 3 residue 535 LEU Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 370 ARG Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 451 ARG Chi-restraints excluded: chain 4 residue 458 LYS Chi-restraints excluded: chain 4 residue 492 HIS Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 533 LEU Chi-restraints excluded: chain 4 residue 564 ILE Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 616 LEU Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 4 residue 798 LEU Chi-restraints excluded: chain 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 132 LEU Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 236 CYS Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 377 SER Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 444 SER Chi-restraints excluded: chain 5 residue 449 LEU Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 575 ILE Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 594 ILE Chi-restraints excluded: chain 5 residue 648 ILE Chi-restraints excluded: chain 5 residue 676 HIS Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 348 VAL Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 457 CYS Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 540 HIS Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 572 CYS Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 641 PHE Chi-restraints excluded: chain 6 residue 646 ILE Chi-restraints excluded: chain 6 residue 751 LEU Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 83 ASP Chi-restraints excluded: chain 7 residue 158 THR Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 269 VAL Chi-restraints excluded: chain 7 residue 279 THR Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 315 ILE Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 416 LYS Chi-restraints excluded: chain 7 residue 464 VAL Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 601 LEU Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 702 PHE Chi-restraints excluded: chain C residue 746 PHE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 478 CYS Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 598 THR Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 641 PHE Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 700 ASN Chi-restraints excluded: chain E residue 751 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 464 VAL Chi-restraints excluded: chain F residue 473 ILE Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 601 LEU Chi-restraints excluded: chain F residue 692 ILE Chi-restraints excluded: chain F residue 696 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 675 optimal weight: 0.3980 chunk 711 optimal weight: 3.9990 chunk 648 optimal weight: 6.9990 chunk 691 optimal weight: 0.4980 chunk 710 optimal weight: 3.9990 chunk 416 optimal weight: 8.9990 chunk 301 optimal weight: 6.9990 chunk 543 optimal weight: 10.0000 chunk 212 optimal weight: 0.6980 chunk 624 optimal weight: 5.9990 chunk 654 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 51 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS B 51 ASN C 651 GLN E 669 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 63714 Z= 0.190 Angle : 0.732 12.451 86712 Z= 0.368 Chirality : 0.045 0.267 10082 Planarity : 0.004 0.063 10746 Dihedral : 14.237 129.802 9761 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 3.22 % Allowed : 19.96 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.41 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.10), residues: 7548 helix: 0.98 (0.10), residues: 2656 sheet: -1.68 (0.16), residues: 1120 loop : -2.52 (0.09), residues: 3772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 476 HIS 0.006 0.001 HIS 3 530 PHE 0.016 0.001 PHE F 526 TYR 0.014 0.001 TYR 2 385 ARG 0.016 0.000 ARG 5 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 717 time to evaluate : 5.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 255 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8357 (tt) REVERT: 2 302 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7532 (t) REVERT: 2 392 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7806 (tm-30) REVERT: 2 614 ASP cc_start: 0.8149 (p0) cc_final: 0.7352 (t0) REVERT: 3 34 THR cc_start: 0.7668 (m) cc_final: 0.7145 (m) REVERT: 3 97 ILE cc_start: 0.9093 (mt) cc_final: 0.8827 (pt) REVERT: 3 117 GLU cc_start: 0.8544 (pt0) cc_final: 0.8249 (pt0) REVERT: 3 234 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7085 (mm-30) REVERT: 3 261 MET cc_start: 0.8137 (ttp) cc_final: 0.7678 (ptp) REVERT: 3 264 MET cc_start: 0.7976 (mtt) cc_final: 0.7342 (mtt) REVERT: 3 279 ASP cc_start: 0.7637 (m-30) cc_final: 0.7208 (m-30) REVERT: 3 346 ASP cc_start: 0.7439 (m-30) cc_final: 0.7072 (m-30) REVERT: 3 482 ASP cc_start: 0.8134 (p0) cc_final: 0.7191 (t0) REVERT: 3 535 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8443 (pp) REVERT: 4 194 PHE cc_start: 0.8705 (t80) cc_final: 0.8338 (t80) REVERT: 4 206 ARG cc_start: 0.8705 (mmt90) cc_final: 0.8477 (mpt180) REVERT: 4 273 ASP cc_start: 0.8377 (m-30) cc_final: 0.8065 (m-30) REVERT: 4 370 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7939 (ptm-80) REVERT: 4 401 GLU cc_start: 0.8566 (pm20) cc_final: 0.8224 (pm20) REVERT: 4 533 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7247 (pt) REVERT: 4 561 ASP cc_start: 0.6706 (t0) cc_final: 0.6347 (p0) REVERT: 4 637 MET cc_start: 0.8125 (mmm) cc_final: 0.7753 (ttp) REVERT: 4 702 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8329 (m-10) REVERT: 4 780 MET cc_start: 0.7565 (mmp) cc_final: 0.7102 (mmm) REVERT: 5 65 MET cc_start: 0.8079 (ttp) cc_final: 0.7273 (mtp) REVERT: 5 76 TYR cc_start: 0.8317 (t80) cc_final: 0.7552 (t80) REVERT: 5 234 LYS cc_start: 0.6764 (pptt) cc_final: 0.6273 (ptpt) REVERT: 5 449 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7888 (tt) REVERT: 5 458 MET cc_start: 0.7505 (ptp) cc_final: 0.7063 (ptp) REVERT: 5 465 GLU cc_start: 0.7791 (tp30) cc_final: 0.7499 (tp30) REVERT: 5 469 MET cc_start: 0.8881 (mmt) cc_final: 0.8660 (mmt) REVERT: 5 513 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8507 (pp) REVERT: 5 676 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7216 (t-170) REVERT: 5 689 MET cc_start: 0.8598 (mmm) cc_final: 0.8011 (mtt) REVERT: 6 175 TYR cc_start: 0.8437 (t80) cc_final: 0.8129 (t80) REVERT: 6 296 ARG cc_start: 0.7438 (ttm170) cc_final: 0.6950 (ttm-80) REVERT: 6 379 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8689 (m) REVERT: 6 540 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.6601 (p90) REVERT: 6 646 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6206 (mm) REVERT: 6 777 TYR cc_start: 0.7406 (t80) cc_final: 0.7156 (t80) REVERT: 7 298 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8998 (pp) REVERT: 7 394 THR cc_start: 0.6483 (OUTLIER) cc_final: 0.6151 (m) REVERT: 7 443 ARG cc_start: 0.7849 (tmm-80) cc_final: 0.7318 (tmm-80) REVERT: 7 529 MET cc_start: 0.8499 (mmt) cc_final: 0.7918 (mmt) REVERT: 7 533 ASP cc_start: 0.8605 (t70) cc_final: 0.8230 (t70) REVERT: 7 675 MET cc_start: 0.5834 (mtt) cc_final: 0.5206 (tpt) REVERT: A 255 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8411 (tt) REVERT: A 302 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7481 (t) REVERT: A 781 MET cc_start: 0.7758 (mtt) cc_final: 0.7219 (ptt) REVERT: B 234 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7019 (mm-30) REVERT: B 279 ASP cc_start: 0.7712 (m-30) cc_final: 0.7280 (m-30) REVERT: B 346 ASP cc_start: 0.7391 (m-30) cc_final: 0.7041 (m-30) REVERT: B 482 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: B 490 MET cc_start: 0.8848 (tpp) cc_final: 0.8589 (tpp) REVERT: C 273 ASP cc_start: 0.8525 (m-30) cc_final: 0.8219 (m-30) REVERT: C 401 GLU cc_start: 0.8494 (pm20) cc_final: 0.8205 (pm20) REVERT: C 561 ASP cc_start: 0.6803 (t0) cc_final: 0.6300 (p0) REVERT: C 780 MET cc_start: 0.7411 (mmp) cc_final: 0.6882 (mmm) REVERT: D 65 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7044 (mtp) REVERT: D 76 TYR cc_start: 0.8182 (t80) cc_final: 0.7469 (t80) REVERT: D 234 LYS cc_start: 0.6582 (pptt) cc_final: 0.5925 (ptpt) REVERT: D 260 GLU cc_start: 0.8179 (tp30) cc_final: 0.7949 (tp30) REVERT: D 454 GLN cc_start: 0.8190 (tt0) cc_final: 0.7941 (tt0) REVERT: D 469 MET cc_start: 0.9001 (mmt) cc_final: 0.8717 (mmt) REVERT: D 513 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8540 (pp) REVERT: D 676 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7478 (t-170) REVERT: D 689 MET cc_start: 0.8509 (mmm) cc_final: 0.7949 (mtt) REVERT: E 175 TYR cc_start: 0.8384 (t80) cc_final: 0.8067 (t80) REVERT: E 261 ARG cc_start: 0.4122 (mpt180) cc_final: 0.3614 (mtt90) REVERT: E 379 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8668 (m) REVERT: E 527 ASP cc_start: 0.8600 (t0) cc_final: 0.8304 (t70) REVERT: E 540 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6674 (p90) REVERT: E 646 ILE cc_start: 0.6359 (OUTLIER) cc_final: 0.5877 (mm) REVERT: F 247 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7302 (ttm-80) REVERT: F 298 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8971 (pp) REVERT: F 393 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7062 (tt) REVERT: F 394 THR cc_start: 0.6582 (OUTLIER) cc_final: 0.6164 (m) REVERT: F 443 ARG cc_start: 0.7907 (tmm-80) cc_final: 0.7373 (tmm-80) REVERT: F 541 MET cc_start: 0.8270 (mmt) cc_final: 0.8048 (mmt) REVERT: F 675 MET cc_start: 0.5746 (mtt) cc_final: 0.5443 (ttt) outliers start: 213 outliers final: 157 residues processed: 883 average time/residue: 0.5377 time to fit residues: 833.0686 Evaluate side-chains 869 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 686 time to evaluate : 5.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 306 LEU Chi-restraints excluded: chain 2 residue 314 LEU Chi-restraints excluded: chain 2 residue 347 ILE Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 455 SER Chi-restraints excluded: chain 2 residue 523 VAL Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 806 THR Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 129 LEU Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 233 THR Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 502 ILE Chi-restraints excluded: chain 3 residue 533 ILE Chi-restraints excluded: chain 3 residue 535 LEU Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 370 ARG Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 451 ARG Chi-restraints excluded: chain 4 residue 492 HIS Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 533 LEU Chi-restraints excluded: chain 4 residue 564 ILE Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 616 LEU Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 236 CYS Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 377 SER Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 444 SER Chi-restraints excluded: chain 5 residue 449 LEU Chi-restraints excluded: chain 5 residue 478 CYS Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 575 ILE Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 594 ILE Chi-restraints excluded: chain 5 residue 648 ILE Chi-restraints excluded: chain 5 residue 668 LEU Chi-restraints excluded: chain 5 residue 676 HIS Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 457 CYS Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 540 HIS Chi-restraints excluded: chain 6 residue 559 THR Chi-restraints excluded: chain 6 residue 572 CYS Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 641 PHE Chi-restraints excluded: chain 6 residue 646 ILE Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 117 PHE Chi-restraints excluded: chain 7 residue 158 THR Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 269 VAL Chi-restraints excluded: chain 7 residue 279 THR Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 315 ILE Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 416 LYS Chi-restraints excluded: chain 7 residue 464 VAL Chi-restraints excluded: chain 7 residue 473 ILE Chi-restraints excluded: chain 7 residue 491 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 601 LEU Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 540 HIS Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 598 THR Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 641 PHE Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 797 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 117 PHE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 464 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 601 LEU Chi-restraints excluded: chain F residue 696 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 689 optimal weight: 1.9990 chunk 454 optimal weight: 0.7980 chunk 731 optimal weight: 5.9990 chunk 446 optimal weight: 0.8980 chunk 346 optimal weight: 8.9990 chunk 508 optimal weight: 1.9990 chunk 767 optimal weight: 20.0000 chunk 706 optimal weight: 2.9990 chunk 610 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 471 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 51 ASN ** 4 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 514 ASN ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN C 651 GLN E 669 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 63714 Z= 0.180 Angle : 0.738 12.941 86712 Z= 0.368 Chirality : 0.044 0.339 10082 Planarity : 0.004 0.063 10746 Dihedral : 14.108 129.497 9760 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.26 % Favored : 90.71 % Rotamer: Outliers : 2.72 % Allowed : 20.60 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.41 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.10), residues: 7548 helix: 1.10 (0.10), residues: 2652 sheet: -1.55 (0.16), residues: 1070 loop : -2.43 (0.09), residues: 3826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.006 0.001 HIS 3 530 PHE 0.022 0.001 PHE A 520 TYR 0.014 0.001 TYR A 555 ARG 0.017 0.000 ARG 5 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15096 Ramachandran restraints generated. 7548 Oldfield, 0 Emsley, 7548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 746 time to evaluate : 5.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 255 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8329 (tt) REVERT: 2 302 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7174 (p) REVERT: 2 306 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6581 (mm) REVERT: 2 392 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7874 (tm-30) REVERT: 2 501 MET cc_start: 0.7704 (tpp) cc_final: 0.7356 (tpp) REVERT: 2 614 ASP cc_start: 0.8087 (p0) cc_final: 0.7278 (t0) REVERT: 3 34 THR cc_start: 0.7609 (m) cc_final: 0.7097 (m) REVERT: 3 97 ILE cc_start: 0.9053 (mt) cc_final: 0.8781 (mm) REVERT: 3 117 GLU cc_start: 0.8445 (pt0) cc_final: 0.8167 (pt0) REVERT: 3 234 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7080 (mm-30) REVERT: 3 261 MET cc_start: 0.8051 (ttp) cc_final: 0.7611 (ptp) REVERT: 3 264 MET cc_start: 0.7965 (mtt) cc_final: 0.7321 (mtt) REVERT: 3 279 ASP cc_start: 0.7582 (m-30) cc_final: 0.7134 (m-30) REVERT: 3 346 ASP cc_start: 0.7409 (m-30) cc_final: 0.7049 (m-30) REVERT: 3 482 ASP cc_start: 0.8107 (p0) cc_final: 0.7162 (t0) REVERT: 3 535 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8384 (pp) REVERT: 4 194 PHE cc_start: 0.8713 (t80) cc_final: 0.8373 (t80) REVERT: 4 206 ARG cc_start: 0.8621 (mmt90) cc_final: 0.8377 (mpt180) REVERT: 4 273 ASP cc_start: 0.8340 (m-30) cc_final: 0.8019 (m-30) REVERT: 4 370 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7884 (ptm-80) REVERT: 4 533 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7137 (pt) REVERT: 4 561 ASP cc_start: 0.6640 (t0) cc_final: 0.6292 (p0) REVERT: 4 637 MET cc_start: 0.8246 (mmm) cc_final: 0.7979 (mmt) REVERT: 4 780 MET cc_start: 0.7518 (mmp) cc_final: 0.7101 (mmm) REVERT: 5 65 MET cc_start: 0.8047 (ttp) cc_final: 0.7277 (mtp) REVERT: 5 76 TYR cc_start: 0.8287 (t80) cc_final: 0.7598 (t80) REVERT: 5 234 LYS cc_start: 0.6776 (pptt) cc_final: 0.6179 (ptpt) REVERT: 5 449 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7746 (tt) REVERT: 5 458 MET cc_start: 0.7586 (ptp) cc_final: 0.7119 (ptp) REVERT: 5 469 MET cc_start: 0.8892 (mmt) cc_final: 0.8679 (mmt) REVERT: 5 486 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7779 (ttp80) REVERT: 5 513 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8634 (pp) REVERT: 5 676 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7235 (t-170) REVERT: 5 689 MET cc_start: 0.8565 (mmm) cc_final: 0.7996 (mtt) REVERT: 6 261 ARG cc_start: 0.3710 (mpt180) cc_final: 0.3033 (mtt90) REVERT: 6 379 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8666 (m) REVERT: 6 646 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6207 (mm) REVERT: 6 777 TYR cc_start: 0.7350 (t80) cc_final: 0.7124 (t80) REVERT: 6 806 LEU cc_start: 0.8583 (mm) cc_final: 0.8333 (mm) REVERT: 7 298 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8968 (pp) REVERT: 7 394 THR cc_start: 0.6375 (OUTLIER) cc_final: 0.6013 (m) REVERT: 7 402 MET cc_start: 0.8061 (mmm) cc_final: 0.7439 (mmm) REVERT: 7 443 ARG cc_start: 0.7855 (tmm-80) cc_final: 0.7321 (tmm-80) REVERT: 7 602 ASP cc_start: 0.6744 (t0) cc_final: 0.6311 (p0) REVERT: 7 675 MET cc_start: 0.5778 (mtt) cc_final: 0.5131 (tpt) REVERT: A 255 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 302 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7565 (t) REVERT: B 234 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6967 (mm-30) REVERT: B 279 ASP cc_start: 0.7601 (m-30) cc_final: 0.7185 (m-30) REVERT: B 346 ASP cc_start: 0.7405 (m-30) cc_final: 0.7070 (m-30) REVERT: B 482 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: B 490 MET cc_start: 0.8862 (tpp) cc_final: 0.8630 (tpp) REVERT: C 273 ASP cc_start: 0.8451 (m-30) cc_final: 0.8139 (m-30) REVERT: C 401 GLU cc_start: 0.8440 (pm20) cc_final: 0.8180 (pm20) REVERT: C 561 ASP cc_start: 0.6786 (t0) cc_final: 0.6299 (p0) REVERT: C 633 GLU cc_start: 0.7282 (tp30) cc_final: 0.6941 (tm-30) REVERT: C 780 MET cc_start: 0.7386 (mmp) cc_final: 0.6895 (mmm) REVERT: D 65 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7080 (mtp) REVERT: D 76 TYR cc_start: 0.8145 (t80) cc_final: 0.7447 (t80) REVERT: D 234 LYS cc_start: 0.6608 (pptt) cc_final: 0.6120 (ptpt) REVERT: D 260 GLU cc_start: 0.8216 (tp30) cc_final: 0.8001 (tp30) REVERT: D 454 GLN cc_start: 0.8374 (tt0) cc_final: 0.7708 (pp30) REVERT: D 469 MET cc_start: 0.8984 (mmt) cc_final: 0.8737 (mmt) REVERT: D 513 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8478 (pp) REVERT: D 676 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7429 (t-170) REVERT: D 689 MET cc_start: 0.8511 (mmm) cc_final: 0.7934 (mtt) REVERT: E 175 TYR cc_start: 0.8298 (t80) cc_final: 0.7997 (t80) REVERT: E 261 ARG cc_start: 0.4109 (mpt180) cc_final: 0.3560 (mtt90) REVERT: E 296 ARG cc_start: 0.7367 (ttm170) cc_final: 0.7158 (ttm-80) REVERT: E 379 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8642 (m) REVERT: E 527 ASP cc_start: 0.8600 (t0) cc_final: 0.8317 (t70) REVERT: E 646 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.5934 (mm) REVERT: F 298 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8947 (pp) REVERT: F 393 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7069 (tt) REVERT: F 394 THR cc_start: 0.6573 (OUTLIER) cc_final: 0.6131 (m) REVERT: F 443 ARG cc_start: 0.7890 (tmm-80) cc_final: 0.7373 (tmm-80) REVERT: F 541 MET cc_start: 0.8205 (mmt) cc_final: 0.7982 (mmt) REVERT: F 675 MET cc_start: 0.5719 (mtt) cc_final: 0.5171 (tpt) outliers start: 180 outliers final: 134 residues processed: 884 average time/residue: 0.5844 time to fit residues: 909.1461 Evaluate side-chains 841 residues out of total 6746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 683 time to evaluate : 5.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 255 ILE Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 306 LEU Chi-restraints excluded: chain 2 residue 314 LEU Chi-restraints excluded: chain 2 residue 402 LEU Chi-restraints excluded: chain 2 residue 523 VAL Chi-restraints excluded: chain 2 residue 636 ILE Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 675 SER Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 129 LEU Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 176 LEU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 221 LEU Chi-restraints excluded: chain 3 residue 233 THR Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 502 ILE Chi-restraints excluded: chain 3 residue 533 ILE Chi-restraints excluded: chain 3 residue 535 LEU Chi-restraints excluded: chain 4 residue 249 LEU Chi-restraints excluded: chain 4 residue 370 ARG Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 442 ILE Chi-restraints excluded: chain 4 residue 492 HIS Chi-restraints excluded: chain 4 residue 522 LEU Chi-restraints excluded: chain 4 residue 533 LEU Chi-restraints excluded: chain 4 residue 564 ILE Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 634 PHE Chi-restraints excluded: chain 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 183 CYS Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 236 CYS Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 377 SER Chi-restraints excluded: chain 5 residue 405 ARG Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 449 LEU Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 575 ILE Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 5 residue 594 ILE Chi-restraints excluded: chain 5 residue 648 ILE Chi-restraints excluded: chain 5 residue 668 LEU Chi-restraints excluded: chain 5 residue 676 HIS Chi-restraints excluded: chain 6 residue 153 ILE Chi-restraints excluded: chain 6 residue 170 ILE Chi-restraints excluded: chain 6 residue 305 TYR Chi-restraints excluded: chain 6 residue 370 THR Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 403 VAL Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 525 ILE Chi-restraints excluded: chain 6 residue 572 CYS Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 628 LEU Chi-restraints excluded: chain 6 residue 641 PHE Chi-restraints excluded: chain 6 residue 646 ILE Chi-restraints excluded: chain 6 residue 751 LEU Chi-restraints excluded: chain 6 residue 766 THR Chi-restraints excluded: chain 7 residue 21 ILE Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 269 VAL Chi-restraints excluded: chain 7 residue 279 THR Chi-restraints excluded: chain 7 residue 298 LEU Chi-restraints excluded: chain 7 residue 315 ILE Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 394 THR Chi-restraints excluded: chain 7 residue 416 LYS Chi-restraints excluded: chain 7 residue 464 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 601 LEU Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 492 HIS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 430 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 559 THR Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 589 VAL Chi-restraints excluded: chain E residue 598 THR Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 641 PHE Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 797 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 393 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 464 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 561 THR Chi-restraints excluded: chain F residue 578 LEU Chi-restraints excluded: chain F residue 601 LEU Chi-restraints excluded: chain F residue 696 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 374 optimal weight: 0.0970 chunk 485 optimal weight: 9.9990 chunk 650 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 563 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 169 optimal weight: 0.0370 chunk 611 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 chunk 628 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 overall best weight: 0.9458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 51 ASN ** 4 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN C 651 GLN E 669 HIS F 336 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.141915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110348 restraints weight = 122530.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110860 restraints weight = 88379.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111256 restraints weight = 94843.756| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 63714 Z= 0.177 Angle : 0.744 13.172 86712 Z= 0.371 Chirality : 0.044 0.323 10082 Planarity : 0.004 0.063 10746 Dihedral : 14.027 129.839 9758 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.65 % Allowed : 21.07 % Favored : 76.29 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.41 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.10), residues: 7548 helix: 1.15 (0.10), residues: 2656 sheet: -1.46 (0.16), residues: 1070 loop : -2.39 (0.09), residues: 3822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 476 HIS 0.006 0.001 HIS 3 530 PHE 0.016 0.001 PHE 7 526 TYR 0.017 0.001 TYR 6 757 ARG 0.010 0.000 ARG 5 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14860.06 seconds wall clock time: 257 minutes 32.45 seconds (15452.45 seconds total)