Starting phenix.real_space_refine on Sun Jan 19 11:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5bk4_9400/01_2025/5bk4_9400.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bk4_9400/01_2025/5bk4_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/cci-nas-00/data/ceres_data/5bk4_9400/01_2025/5bk4_9400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bk4_9400/01_2025/5bk4_9400.map" model { file = "/net/cci-nas-00/data/ceres_data/5bk4_9400/01_2025/5bk4_9400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bk4_9400/01_2025/5bk4_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-5571/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: 27.68, per 1000 atoms: 0.44 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: 11.05 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: 14.55 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: 22.45 Time building geometry restraints manager: 13.25 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: 0.11 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: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.070 Extract box with map and model: 1.840 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 111.840 Find NCS groups from input model: 4.010 Set up NCS constraints: 0.330 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:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.800 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 84 poor density : 1666 time to evaluate : 5.170 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: 0.6560 time to fit residues: 1840.3944 Evaluate side-chains 867 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 844 time to evaluate : 5.289 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.142341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111256 restraints weight = 122505.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.110663 restraints weight = 85751.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.111488 restraints weight = 90820.357| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 to be fit. rotamer outliers: 220 poor density : 1014 time to evaluate : 5.320 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: 0.8092 (m) cc_final: 0.7806 (p) REVERT: 2 302 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.7953 (p) REVERT: 2 644 CYS cc_start: 0.7954 (m) cc_final: 0.7722 (m) REVERT: 3 185 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9139 (mt) REVERT: 3 279 ASP cc_start: 0.7933 (m-30) cc_final: 0.7548 (m-30) REVERT: 3 307 ASN cc_start: 0.8547 (t0) cc_final: 0.8310 (t0) REVERT: 3 325 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9082 (m) REVERT: 3 330 HIS cc_start: 0.7917 (t-170) cc_final: 0.6680 (p-80) REVERT: 3 346 ASP cc_start: 0.7235 (m-30) cc_final: 0.6820 (m-30) REVERT: 3 364 SER cc_start: 0.9071 (m) cc_final: 0.8835 (p) REVERT: 3 482 ASP cc_start: 0.8150 (p0) cc_final: 0.7681 (m-30) REVERT: 3 497 ILE cc_start: 0.8950 (mp) cc_final: 0.8598 (mm) REVERT: 3 535 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8654 (pp) REVERT: 3 685 ASP cc_start: 0.8234 (t0) cc_final: 0.8000 (t0) REVERT: 4 206 ARG cc_start: 0.8738 (mmt90) cc_final: 0.8507 (mpt180) REVERT: 4 273 ASP cc_start: 0.8212 (m-30) cc_final: 0.7977 (m-30) REVERT: 4 473 ARG cc_start: 0.8478 (mmm160) cc_final: 0.8167 (mmm160) REVERT: 4 506 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8585 (tm) REVERT: 4 702 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8505 (m-10) REVERT: 4 728 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7223 (t80) REVERT: 4 780 MET cc_start: 0.7472 (mmp) cc_final: 0.7110 (mmm) REVERT: 5 65 MET cc_start: 0.7553 (ttp) cc_final: 0.7295 (ttp) REVERT: 5 76 TYR cc_start: 0.7750 (t80) cc_final: 0.7316 (t80) REVERT: 5 234 LYS cc_start: 0.7046 (pptt) cc_final: 0.6428 (ptpt) REVERT: 5 465 GLU cc_start: 0.8092 (tp30) cc_final: 0.7617 (tp30) REVERT: 5 469 MET cc_start: 0.8935 (mmt) cc_final: 0.8573 (mmt) REVERT: 5 513 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8523 (pp) REVERT: 5 517 THR cc_start: 0.9235 (p) cc_final: 0.8964 (p) REVERT: 5 565 ASP cc_start: 0.8650 (m-30) cc_final: 0.8404 (p0) REVERT: 5 689 MET cc_start: 0.8278 (mmm) cc_final: 0.8033 (mtt) REVERT: 6 175 TYR cc_start: 0.8356 (t80) cc_final: 0.7952 (t80) REVERT: 6 278 ASP cc_start: 0.7903 (t0) cc_final: 0.7339 (t0) REVERT: 6 379 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8770 (m) REVERT: 6 514 ASN cc_start: 0.8359 (m-40) cc_final: 0.8120 (t0) REVERT: 6 525 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8055 (pt) REVERT: 6 621 TYR cc_start: 0.5018 (p90) cc_final: 0.3916 (p90) REVERT: 6 636 CYS cc_start: 0.8511 (t) cc_final: 0.8101 (p) REVERT: 6 805 ARG cc_start: 0.8135 (ptp-170) cc_final: 0.7646 (mtt180) REVERT: 6 818 GLU cc_start: 0.6864 (mp0) cc_final: 0.6630 (tp30) REVERT: 7 84 ASP cc_start: 0.7682 (m-30) cc_final: 0.7418 (m-30) REVERT: 7 298 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8906 (pp) REVERT: 7 442 LYS cc_start: 0.7572 (tptt) cc_final: 0.7144 (tttt) REVERT: 7 529 MET cc_start: 0.8685 (mmt) cc_final: 0.8152 (mmt) REVERT: 7 675 MET cc_start: 0.6118 (mtt) cc_final: 0.5752 (ttt) REVERT: A 279 THR cc_start: 0.8110 (m) cc_final: 0.7820 (p) REVERT: A 302 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7854 (p) REVERT: A 609 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7176 (m-10) REVERT: A 628 SER cc_start: 0.8733 (p) cc_final: 0.8351 (m) REVERT: B 211 TYR cc_start: 0.8559 (t80) cc_final: 0.8324 (t80) REVERT: B 234 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6854 (mm-30) REVERT: B 279 ASP cc_start: 0.7834 (m-30) cc_final: 0.7517 (m-30) REVERT: B 325 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.9070 (m) REVERT: B 346 ASP cc_start: 0.7384 (m-30) cc_final: 0.7060 (m-30) REVERT: B 364 SER cc_start: 0.8929 (m) cc_final: 0.8649 (p) REVERT: B 407 MET cc_start: 0.7647 (mtp) cc_final: 0.7375 (mtp) REVERT: B 490 MET cc_start: 0.8359 (tpp) cc_final: 0.8116 (tpp) REVERT: B 522 GLN cc_start: 0.8125 (mp10) cc_final: 0.7480 (tm-30) REVERT: C 273 ASP cc_start: 0.8128 (m-30) cc_final: 0.7886 (m-30) REVERT: C 473 ARG cc_start: 0.8500 (mmm160) cc_final: 0.8162 (mmm160) REVERT: C 506 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8650 (tm) REVERT: C 702 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8234 (m-10) REVERT: C 780 MET cc_start: 0.7212 (mmp) cc_final: 0.6704 (mmm) REVERT: D 65 MET cc_start: 0.7560 (ttp) cc_final: 0.7313 (ttp) REVERT: D 76 TYR cc_start: 0.7786 (t80) cc_final: 0.7349 (t80) REVERT: D 196 ASN cc_start: 0.8175 (m-40) cc_final: 0.7965 (p0) REVERT: D 234 LYS cc_start: 0.6855 (pptt) cc_final: 0.6336 (ptpt) REVERT: D 390 CYS cc_start: 0.8418 (p) cc_final: 0.8192 (m) REVERT: D 458 MET cc_start: 0.7321 (ptp) cc_final: 0.6897 (ppp) REVERT: D 465 GLU cc_start: 0.7861 (tp30) cc_final: 0.7409 (tp30) REVERT: D 469 MET cc_start: 0.9085 (mmt) cc_final: 0.8873 (mmt) REVERT: D 513 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8488 (pp) REVERT: D 681 ILE cc_start: 0.8522 (mm) cc_final: 0.8203 (mt) REVERT: E 175 TYR cc_start: 0.8295 (t80) cc_final: 0.7928 (t80) REVERT: E 261 ARG cc_start: 0.3487 (mpt180) cc_final: 0.2633 (mtt90) REVERT: E 278 ASP cc_start: 0.7855 (t0) cc_final: 0.7288 (t0) REVERT: E 379 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8739 (m) REVERT: E 525 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8072 (pt) REVERT: E 621 TYR cc_start: 0.5044 (p90) cc_final: 0.4478 (p90) REVERT: E 636 CYS cc_start: 0.8885 (t) cc_final: 0.8005 (p) REVERT: E 794 ARG cc_start: 0.6697 (tpm170) cc_final: 0.6345 (tpm170) REVERT: F 84 ASP cc_start: 0.7605 (m-30) cc_final: 0.7334 (m-30) REVERT: F 298 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8913 (pp) REVERT: F 402 MET cc_start: 0.8054 (tpp) cc_final: 0.7784 (tpp) REVERT: F 442 LYS cc_start: 0.7442 (tptt) cc_final: 0.7046 (tttt) REVERT: F 529 MET cc_start: 0.8709 (mmt) cc_final: 0.8192 (mmt) REVERT: F 541 MET cc_start: 0.8034 (mmt) cc_final: 0.7657 (mmt) REVERT: F 675 MET cc_start: 0.5976 (mtt) cc_final: 0.5592 (ttt) outliers start: 220 outliers final: 95 residues processed: 1168 average time/residue: 0.5597 time to fit residues: 1115.8119 Evaluate side-chains 870 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 755 time to evaluate : 5.259 ------------------------------------------------------------------------------- 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 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 584 optimal weight: 0.0970 chunk 635 optimal weight: 5.9990 chunk 338 optimal weight: 3.9990 chunk 480 optimal weight: 7.9990 chunk 436 optimal weight: 6.9990 chunk 756 optimal weight: 6.9990 chunk 297 optimal weight: 0.0970 chunk 346 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 545 optimal weight: 1.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 641 GLN 2 849 GLN 3 51 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 A 849 GLN B 51 ASN B 569 HIS ** C 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 669 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.142146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.110864 restraints weight = 122750.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110245 restraints weight = 82904.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110971 restraints weight = 89625.150| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 63714 Z= 0.187 Angle : 0.728 12.112 86712 Z= 0.375 Chirality : 0.045 0.212 10082 Planarity : 0.005 0.065 10746 Dihedral : 14.820 127.706 9772 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.63 % Allowed : 14.35 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.36 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.66 (0.09), residues: 7548 helix: -0.35 (0.10), residues: 2684 sheet: -2.13 (0.16), residues: 1056 loop : -2.79 (0.09), residues: 3808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 111 HIS 0.008 0.001 HIS B 569 PHE 0.022 0.001 PHE D 38 TYR 0.018 0.001 TYR 4 774 ARG 0.012 0.000 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 1114 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 874 time to evaluate : 5.360 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: 2 279 THR cc_start: 0.8040 (m) cc_final: 0.7787 (p) REVERT: 2 302 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.8009 (t) REVERT: 2 581 ARG cc_start: 0.7637 (ptp90) cc_final: 0.7165 (ttp80) REVERT: 2 644 CYS cc_start: 0.7706 (m) cc_final: 0.7451 (m) REVERT: 3 29 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7704 (tm-30) REVERT: 3 185 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9117 (mt) REVERT: 3 234 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7005 (mm-30) REVERT: 3 279 ASP cc_start: 0.7858 (m-30) cc_final: 0.7508 (m-30) REVERT: 3 330 HIS cc_start: 0.8009 (t-170) cc_final: 0.6834 (p-80) REVERT: 3 346 ASP cc_start: 0.7421 (m-30) cc_final: 0.6957 (m-30) REVERT: 3 364 SER cc_start: 0.9078 (m) cc_final: 0.8838 (p) REVERT: 3 535 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8611 (pp) REVERT: 4 206 ARG cc_start: 0.8821 (mmt90) cc_final: 0.8493 (mpt180) REVERT: 4 273 ASP cc_start: 0.8176 (m-30) cc_final: 0.7936 (m-30) REVERT: 4 473 ARG cc_start: 0.8587 (mmm160) cc_final: 0.8311 (mmm160) REVERT: 4 693 ASP cc_start: 0.6572 (t0) cc_final: 0.6317 (t70) REVERT: 4 702 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8593 (m-10) REVERT: 4 728 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7159 (t80) REVERT: 4 780 MET cc_start: 0.7514 (mmp) cc_final: 0.7249 (mmm) REVERT: 5 31 PHE cc_start: 0.7924 (m-80) cc_final: 0.7672 (m-10) REVERT: 5 76 TYR cc_start: 0.7980 (t80) cc_final: 0.7646 (t80) REVERT: 5 234 LYS cc_start: 0.7067 (pptt) cc_final: 0.6494 (ptpt) REVERT: 5 329 LYS cc_start: 0.8102 (tptp) cc_final: 0.7901 (mtmm) REVERT: 5 331 LEU cc_start: 0.7925 (pt) cc_final: 0.7519 (pp) REVERT: 5 469 MET cc_start: 0.8895 (mmt) cc_final: 0.8567 (mmt) REVERT: 5 513 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8531 (pp) REVERT: 5 689 MET cc_start: 0.8376 (mmm) cc_final: 0.8144 (mtt) REVERT: 6 175 TYR cc_start: 0.8376 (t80) cc_final: 0.7950 (t80) REVERT: 6 261 ARG cc_start: 0.2952 (mpt180) cc_final: 0.2244 (mtt90) REVERT: 6 278 ASP cc_start: 0.7985 (t0) cc_final: 0.7460 (t0) REVERT: 6 379 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8727 (m) REVERT: 6 514 ASN cc_start: 0.8415 (m-40) cc_final: 0.8117 (t0) REVERT: 6 525 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8031 (pt) REVERT: 6 636 CYS cc_start: 0.8587 (t) cc_final: 0.7974 (p) REVERT: 6 711 LEU cc_start: 0.7319 (tp) cc_final: 0.7116 (tp) REVERT: 6 777 TYR cc_start: 0.7671 (t80) cc_final: 0.7431 (t80) REVERT: 6 805 ARG cc_start: 0.8067 (ptp-170) cc_final: 0.7748 (mtt180) REVERT: 7 256 GLU cc_start: 0.8033 (tp30) cc_final: 0.7157 (tp30) REVERT: 7 298 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8901 (pp) REVERT: 7 402 MET cc_start: 0.8183 (tpp) cc_final: 0.7639 (tpp) REVERT: 7 442 LYS cc_start: 0.7402 (tptt) cc_final: 0.6935 (tttt) REVERT: 7 509 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7643 (mm-30) REVERT: 7 675 MET cc_start: 0.5829 (mtt) cc_final: 0.5521 (ttt) REVERT: A 279 THR cc_start: 0.8124 (m) cc_final: 0.7863 (p) REVERT: A 302 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7978 (t) REVERT: A 581 ARG cc_start: 0.7703 (ptp90) cc_final: 0.7491 (ttp80) REVERT: A 609 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7302 (m-10) REVERT: A 646 ILE cc_start: 0.9295 (mt) cc_final: 0.8999 (tt) REVERT: B 34 THR cc_start: 0.7646 (m) cc_final: 0.7188 (m) REVERT: B 211 TYR cc_start: 0.8328 (t80) cc_final: 0.7948 (t80) REVERT: B 234 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6967 (mm-30) REVERT: B 240 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8595 (mmmm) REVERT: B 261 MET cc_start: 0.8240 (ttp) cc_final: 0.8039 (ptp) REVERT: B 279 ASP cc_start: 0.7922 (m-30) cc_final: 0.7535 (m-30) REVERT: B 346 ASP cc_start: 0.7343 (m-30) cc_final: 0.6961 (m-30) REVERT: B 364 SER cc_start: 0.8882 (m) cc_final: 0.8587 (p) REVERT: C 273 ASP cc_start: 0.8224 (m-30) cc_final: 0.7982 (m-30) REVERT: C 473 ARG cc_start: 0.8622 (mmm160) cc_final: 0.8348 (mmm160) REVERT: C 702 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8318 (m-10) REVERT: C 728 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7146 (t80) REVERT: C 780 MET cc_start: 0.7300 (mmp) cc_final: 0.6738 (mmm) REVERT: D 76 TYR cc_start: 0.7903 (t80) cc_final: 0.7671 (t80) REVERT: D 234 LYS cc_start: 0.6923 (pptt) cc_final: 0.6273 (ptpt) REVERT: D 331 LEU cc_start: 0.7846 (pt) cc_final: 0.7505 (pp) REVERT: D 458 MET cc_start: 0.7367 (ptp) cc_final: 0.7021 (ppp) REVERT: D 465 GLU cc_start: 0.7850 (tp30) cc_final: 0.7387 (tp30) REVERT: D 469 MET cc_start: 0.9066 (mmt) cc_final: 0.8837 (mmt) REVERT: D 513 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8554 (pp) REVERT: E 175 TYR cc_start: 0.8313 (t80) cc_final: 0.7927 (t80) REVERT: E 261 ARG cc_start: 0.3649 (mpt180) cc_final: 0.1868 (mtm-85) REVERT: E 278 ASP cc_start: 0.8007 (t0) cc_final: 0.7482 (t0) REVERT: E 379 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8720 (m) REVERT: E 525 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7545 (tp) REVERT: E 621 TYR cc_start: 0.4970 (p90) cc_final: 0.3722 (p90) REVERT: E 636 CYS cc_start: 0.8817 (t) cc_final: 0.7962 (p) REVERT: E 646 ILE cc_start: 0.6151 (OUTLIER) cc_final: 0.5752 (mm) REVERT: F 84 ASP cc_start: 0.7366 (m-30) cc_final: 0.7035 (m-30) REVERT: F 160 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8178 (tm-30) REVERT: F 256 GLU cc_start: 0.8119 (tp30) cc_final: 0.6656 (tp30) REVERT: F 298 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8933 (pp) REVERT: F 393 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6761 (tt) REVERT: F 442 LYS cc_start: 0.7275 (tptt) cc_final: 0.6824 (tttt) REVERT: F 509 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7783 (mm-30) REVERT: F 529 MET cc_start: 0.8774 (mmt) cc_final: 0.8233 (mmt) REVERT: F 541 MET cc_start: 0.8095 (mmt) cc_final: 0.7767 (mmt) REVERT: F 675 MET cc_start: 0.6038 (mtt) cc_final: 0.5651 (ttt) outliers start: 240 outliers final: 138 residues processed: 1038 average time/residue: 0.5561 time to fit residues: 1000.2965 Evaluate side-chains 885 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 727 time to evaluate : 5.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 219 THR 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 455 SER Chi-restraints excluded: chain 2 residue 519 LEU Chi-restraints excluded: chain 2 residue 556 VAL Chi-restraints excluded: chain 2 residue 637 VAL Chi-restraints excluded: chain 2 residue 641 GLN 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 185 ILE 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 336 VAL 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 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 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 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 264 LEU Chi-restraints excluded: chain 5 residue 377 SER Chi-restraints excluded: chain 5 residue 444 SER Chi-restraints excluded: chain 5 residue 478 CYS Chi-restraints excluded: chain 5 residue 485 MET 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 631 LYS Chi-restraints excluded: chain 5 residue 632 GLN Chi-restraints excluded: chain 6 residue 118 PHE 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 525 ILE 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 25 LEU 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 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 7 residue 696 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 609 PHE 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 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 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 336 VAL 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 385 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 492 HIS 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 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 264 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 478 CYS Chi-restraints excluded: chain D residue 485 MET 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 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 525 ILE 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 751 LEU 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 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 459 MET 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 557 LEU Chi-restraints excluded: chain F residue 561 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 101 optimal weight: 7.9990 chunk 498 optimal weight: 10.0000 chunk 660 optimal weight: 5.9990 chunk 559 optimal weight: 9.9990 chunk 608 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 303 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 220 optimal weight: 0.2980 chunk 246 optimal weight: 8.9990 overall best weight: 6.4588 ------------------------------------------------------------------------------- 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 3 530 HIS 3 531 GLN 4 354 HIS 4 493 ASN ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 424 GLN 6 125 GLN 6 669 HIS 6 700 ASN A 856 GLN B 51 ASN B 492 GLN C 354 HIS C 410 GLN C 493 ASN ** C 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN D 424 GLN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN E 669 HIS E 799 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104832 restraints weight = 123054.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105464 restraints weight = 91830.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.105538 restraints weight = 103328.426| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 63714 Z= 0.410 Angle : 0.836 12.584 86712 Z= 0.433 Chirality : 0.049 0.314 10082 Planarity : 0.006 0.072 10746 Dihedral : 14.919 135.144 9770 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.19 % Favored : 87.78 % Rotamer: Outliers : 5.15 % Allowed : 15.45 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.39 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.49 (0.09), residues: 7548 helix: 0.11 (0.10), residues: 2644 sheet: -2.18 (0.16), residues: 1062 loop : -2.88 (0.09), residues: 3842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 3 111 HIS 0.012 0.002 HIS B 164 PHE 0.025 0.002 PHE 4 439 TYR 0.035 0.002 TYR B 211 ARG 0.022 0.001 ARG D 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 1081 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 340 poor density : 741 time to evaluate : 5.375 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: 2 279 THR cc_start: 0.8186 (m) cc_final: 0.7897 (p) REVERT: 2 302 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7872 (t) REVERT: 2 614 ASP cc_start: 0.7919 (p0) cc_final: 0.7352 (t0) REVERT: 2 781 MET cc_start: 0.7655 (mtt) cc_final: 0.7294 (ptt) REVERT: 3 191 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8121 (mt) REVERT: 3 234 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7219 (mm-30) REVERT: 3 279 ASP cc_start: 0.8077 (m-30) cc_final: 0.7610 (m-30) REVERT: 3 346 ASP cc_start: 0.7478 (m-30) cc_final: 0.7028 (m-30) REVERT: 3 364 SER cc_start: 0.9065 (m) cc_final: 0.8782 (p) REVERT: 3 407 MET cc_start: 0.7941 (mtp) cc_final: 0.7648 (mtp) REVERT: 3 482 ASP cc_start: 0.8250 (p0) cc_final: 0.7657 (t0) REVERT: 3 535 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8657 (pp) REVERT: 4 206 ARG cc_start: 0.8875 (mmt90) cc_final: 0.8568 (mpt180) REVERT: 4 273 ASP cc_start: 0.8306 (m-30) cc_final: 0.8071 (m-30) REVERT: 4 561 ASP cc_start: 0.7143 (t0) cc_final: 0.6664 (p0) REVERT: 4 702 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8423 (m-10) REVERT: 4 780 MET cc_start: 0.7614 (mmp) cc_final: 0.7156 (mmm) REVERT: 5 65 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7388 (mtp) REVERT: 5 76 TYR cc_start: 0.8341 (t80) cc_final: 0.7773 (t80) REVERT: 5 234 LYS cc_start: 0.6755 (pptt) cc_final: 0.6244 (ptpt) REVERT: 5 331 LEU cc_start: 0.8070 (pt) cc_final: 0.7842 (pp) REVERT: 5 449 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8123 (tt) REVERT: 5 454 GLN cc_start: 0.8216 (tt0) cc_final: 0.7627 (tm-30) REVERT: 5 469 MET cc_start: 0.8999 (mmt) cc_final: 0.8753 (mmt) REVERT: 5 513 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8586 (pp) REVERT: 5 689 MET cc_start: 0.8415 (mmm) cc_final: 0.7958 (mtt) REVERT: 6 143 MET cc_start: 0.8366 (ttp) cc_final: 0.8130 (ttp) REVERT: 6 175 TYR cc_start: 0.8692 (t80) cc_final: 0.8397 (t80) REVERT: 6 261 ARG cc_start: 0.3383 (mpt180) cc_final: 0.2709 (mtt90) REVERT: 6 379 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8754 (m) REVERT: 6 519 MET cc_start: 0.6999 (mmt) cc_final: 0.6721 (mmp) REVERT: 6 525 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8195 (pt) REVERT: 6 636 CYS cc_start: 0.8721 (t) cc_final: 0.8066 (p) REVERT: 6 646 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6551 (mm) REVERT: 6 805 ARG cc_start: 0.8195 (ptp-170) cc_final: 0.7859 (mtt180) REVERT: 7 1 MET cc_start: 0.5056 (ptm) cc_final: 0.4243 (ptm) REVERT: 7 64 MET cc_start: 0.8313 (mmp) cc_final: 0.8077 (mmp) REVERT: 7 298 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9028 (pp) REVERT: 7 442 LYS cc_start: 0.7631 (tptt) cc_final: 0.7285 (ttmt) REVERT: 7 529 MET cc_start: 0.8573 (mmt) cc_final: 0.8112 (mmt) REVERT: 7 675 MET cc_start: 0.5853 (mtt) cc_final: 0.5529 (ttt) REVERT: A 279 THR cc_start: 0.8193 (m) cc_final: 0.7908 (p) REVERT: A 302 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7906 (t) REVERT: A 306 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7046 (mm) REVERT: B 191 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8094 (mt) REVERT: B 234 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7242 (mm-30) REVERT: B 240 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8513 (mmmm) REVERT: B 279 ASP cc_start: 0.7977 (m-30) cc_final: 0.7579 (m-30) REVERT: B 346 ASP cc_start: 0.7429 (m-30) cc_final: 0.7079 (m-30) REVERT: B 364 SER cc_start: 0.9044 (m) cc_final: 0.8814 (p) REVERT: B 482 ASP cc_start: 0.8149 (p0) cc_final: 0.7461 (m-30) REVERT: B 490 MET cc_start: 0.8848 (tpp) cc_final: 0.8515 (tpp) REVERT: B 535 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8688 (pp) REVERT: C 273 ASP cc_start: 0.8244 (m-30) cc_final: 0.8007 (m-30) REVERT: C 561 ASP cc_start: 0.7139 (t0) cc_final: 0.6622 (p0) REVERT: C 702 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8444 (m-10) REVERT: C 780 MET cc_start: 0.7572 (mmp) cc_final: 0.7022 (mmm) REVERT: D 65 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7337 (mtp) REVERT: D 76 TYR cc_start: 0.8293 (t80) cc_final: 0.7711 (t80) REVERT: D 234 LYS cc_start: 0.6765 (pptt) cc_final: 0.6259 (ptpt) REVERT: D 458 MET cc_start: 0.7373 (ptp) cc_final: 0.7134 (ppp) REVERT: D 465 GLU cc_start: 0.8240 (tp30) cc_final: 0.7977 (tp30) REVERT: D 469 MET cc_start: 0.9088 (mmt) cc_final: 0.8814 (mmt) REVERT: D 513 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8749 (pp) REVERT: E 175 TYR cc_start: 0.8665 (t80) cc_final: 0.8402 (t80) REVERT: E 261 ARG cc_start: 0.3877 (mpt180) cc_final: 0.3282 (mtt90) REVERT: E 379 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8739 (m) REVERT: E 428 LYS cc_start: 0.8263 (tptp) cc_final: 0.7753 (tmtt) REVERT: E 519 MET cc_start: 0.6926 (mmt) cc_final: 0.6708 (mmp) REVERT: E 636 CYS cc_start: 0.8852 (t) cc_final: 0.8223 (p) REVERT: F 1 MET cc_start: 0.4914 (ptm) cc_final: 0.4102 (ptm) REVERT: F 298 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9045 (pp) REVERT: F 442 LYS cc_start: 0.7409 (tptt) cc_final: 0.7039 (ttmt) REVERT: F 541 MET cc_start: 0.8325 (mmt) cc_final: 0.7994 (mmt) REVERT: F 675 MET cc_start: 0.5847 (mtt) cc_final: 0.5550 (ttt) REVERT: F 711 ASP cc_start: 0.7368 (p0) cc_final: 0.7102 (p0) outliers start: 340 outliers final: 210 residues processed: 995 average time/residue: 0.6090 time to fit residues: 1069.1759 Evaluate side-chains 901 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 670 time to evaluate : 5.365 ------------------------------------------------------------------------------- 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 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 523 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 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 191 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 386 MET Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 430 ILE 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 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 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 458 LYS 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 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 27 ILE Chi-restraints excluded: chain 5 residue 65 MET 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 205 VAL Chi-restraints excluded: chain 5 residue 236 CYS Chi-restraints excluded: chain 5 residue 252 ASP 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 5 residue 681 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 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 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 7 residue 9 GLN 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 158 THR Chi-restraints excluded: chain 7 residue 248 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 258 ILE Chi-restraints excluded: chain 7 residue 263 ASP 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 300 MET 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 459 MET 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 205 ARG 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 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 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 191 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 240 LYS 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 413 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 535 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 433 ILE Chi-restraints excluded: chain C residue 442 ILE 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 746 PHE Chi-restraints excluded: chain C residue 756 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 191 SER Chi-restraints excluded: chain D residue 197 PHE 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 283 THR 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 444 SER Chi-restraints excluded: chain D residue 478 CYS 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 D residue 677 VAL Chi-restraints excluded: chain E residue 106 VAL 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 348 VAL Chi-restraints excluded: chain E residue 370 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 385 SER 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 589 VAL Chi-restraints excluded: chain E residue 598 THR Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 700 ASN Chi-restraints excluded: chain E residue 742 ILE 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 248 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 263 ASP 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 349 VAL Chi-restraints excluded: chain F residue 374 THR 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 658 optimal weight: 20.0000 chunk 726 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 2 optimal weight: 20.0000 chunk 443 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 389 optimal weight: 3.9990 chunk 515 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 ** 3 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 424 GLN 6 149 ASN 6 669 HIS 6 700 ASN 7 544 GLN A 856 GLN B 51 ASN ** C 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN D 576 HIS E 669 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.139052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107258 restraints weight = 122006.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108370 restraints weight = 87789.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108342 restraints weight = 97554.748| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 63714 Z= 0.219 Angle : 0.734 11.992 86712 Z= 0.377 Chirality : 0.045 0.244 10082 Planarity : 0.005 0.061 10746 Dihedral : 14.695 132.666 9770 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 4.52 % Allowed : 16.86 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 2.39 % 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: -2.18 (0.09), residues: 7548 helix: 0.45 (0.10), residues: 2654 sheet: -2.02 (0.16), residues: 1074 loop : -2.76 (0.09), residues: 3820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 111 HIS 0.008 0.001 HIS 4 413 PHE 0.032 0.001 PHE D 31 TYR 0.020 0.001 TYR 3 327 ARG 0.009 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 1028 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 299 poor density : 729 time to evaluate : 5.431 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: 2 279 THR cc_start: 0.8179 (m) cc_final: 0.7953 (p) REVERT: 2 302 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7839 (t) REVERT: 2 306 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6859 (mm) REVERT: 2 392 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7872 (tm-30) REVERT: 2 614 ASP cc_start: 0.7973 (p0) cc_final: 0.7385 (t0) REVERT: 2 781 MET cc_start: 0.7551 (mtt) cc_final: 0.7247 (ptt) REVERT: 3 191 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8068 (mt) REVERT: 3 234 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7028 (mm-30) REVERT: 3 279 ASP cc_start: 0.7912 (m-30) cc_final: 0.7463 (m-30) REVERT: 3 346 ASP cc_start: 0.7377 (m-30) cc_final: 0.6955 (m-30) REVERT: 3 364 SER cc_start: 0.9043 (m) cc_final: 0.8833 (p) REVERT: 3 482 ASP cc_start: 0.8280 (p0) cc_final: 0.7430 (t0) REVERT: 3 535 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8633 (pp) REVERT: 4 206 ARG cc_start: 0.8826 (mmt90) cc_final: 0.8530 (mpt180) REVERT: 4 273 ASP cc_start: 0.8257 (m-30) cc_final: 0.8026 (m-30) REVERT: 4 533 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7363 (pt) REVERT: 4 561 ASP cc_start: 0.6990 (t0) cc_final: 0.6563 (p0) REVERT: 4 637 MET cc_start: 0.8335 (mmm) cc_final: 0.8001 (ttp) REVERT: 4 702 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8307 (m-10) REVERT: 4 780 MET cc_start: 0.7550 (mmp) cc_final: 0.7118 (mmm) REVERT: 5 65 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7056 (mtp) REVERT: 5 76 TYR cc_start: 0.8223 (t80) cc_final: 0.7554 (t80) REVERT: 5 218 GLU cc_start: 0.5260 (OUTLIER) cc_final: 0.2714 (mt-10) REVERT: 5 221 MET cc_start: 0.7678 (mpt) cc_final: 0.7354 (mpt) REVERT: 5 234 LYS cc_start: 0.6756 (pptt) cc_final: 0.6217 (ptpt) REVERT: 5 331 LEU cc_start: 0.7739 (pt) cc_final: 0.7386 (pp) REVERT: 5 454 GLN cc_start: 0.8273 (tt0) cc_final: 0.7079 (tm-30) REVERT: 5 465 GLU cc_start: 0.8027 (tp30) cc_final: 0.6685 (tp30) REVERT: 5 469 MET cc_start: 0.8989 (mmt) cc_final: 0.8755 (mmt) REVERT: 5 513 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8466 (pp) REVERT: 5 661 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7765 (mt-10) REVERT: 5 689 MET cc_start: 0.8348 (mmm) cc_final: 0.8139 (mtt) REVERT: 6 175 TYR cc_start: 0.8512 (t80) cc_final: 0.8184 (t80) REVERT: 6 379 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8754 (m) REVERT: 6 519 MET cc_start: 0.6907 (mmt) cc_final: 0.6636 (mmp) REVERT: 6 525 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8110 (pt) REVERT: 6 636 CYS cc_start: 0.8686 (t) cc_final: 0.7974 (p) REVERT: 6 646 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6431 (mm) REVERT: 6 805 ARG cc_start: 0.8095 (ptp-170) cc_final: 0.7819 (mtt180) REVERT: 7 1 MET cc_start: 0.4782 (ptm) cc_final: 0.3972 (ptm) REVERT: 7 298 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8983 (pp) REVERT: 7 394 THR cc_start: 0.6843 (OUTLIER) cc_final: 0.6540 (m) REVERT: 7 402 MET cc_start: 0.8249 (tpp) cc_final: 0.7752 (tpp) REVERT: 7 499 LYS cc_start: 0.8455 (tppt) cc_final: 0.8157 (tppt) REVERT: 7 529 MET cc_start: 0.8625 (mmt) cc_final: 0.8170 (mmt) REVERT: 7 675 MET cc_start: 0.5682 (mtt) cc_final: 0.5446 (ttt) REVERT: A 279 THR cc_start: 0.8196 (m) cc_final: 0.7965 (p) REVERT: A 302 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7755 (t) REVERT: B 191 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8018 (mt) REVERT: B 234 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7017 (mm-30) REVERT: B 240 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8553 (mmmm) REVERT: B 279 ASP cc_start: 0.7820 (m-30) cc_final: 0.7418 (m-30) REVERT: B 346 ASP cc_start: 0.7354 (m-30) cc_final: 0.6947 (m-30) REVERT: B 482 ASP cc_start: 0.8138 (p0) cc_final: 0.7373 (m-30) REVERT: B 535 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8671 (pp) REVERT: C 273 ASP cc_start: 0.8183 (m-30) cc_final: 0.7966 (m-30) REVERT: C 561 ASP cc_start: 0.7065 (t0) cc_final: 0.6448 (p0) REVERT: C 702 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8312 (m-10) REVERT: C 780 MET cc_start: 0.7573 (mmp) cc_final: 0.7005 (mmm) REVERT: C 803 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6989 (ptp-170) REVERT: D 65 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7076 (mtp) REVERT: D 76 TYR cc_start: 0.8160 (t80) cc_final: 0.7540 (t80) REVERT: D 218 GLU cc_start: 0.5086 (OUTLIER) cc_final: 0.2244 (mt-10) REVERT: D 234 LYS cc_start: 0.6756 (pptt) cc_final: 0.6251 (ptpt) REVERT: D 413 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8040 (mp) REVERT: D 469 MET cc_start: 0.9030 (mmt) cc_final: 0.8804 (mmt) REVERT: D 513 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8702 (pp) REVERT: E 175 TYR cc_start: 0.8474 (t80) cc_final: 0.8171 (t80) REVERT: E 261 ARG cc_start: 0.3954 (mpt180) cc_final: 0.3369 (mtt90) REVERT: E 379 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8751 (m) REVERT: E 428 LYS cc_start: 0.8201 (tptp) cc_final: 0.7571 (tmtt) REVERT: E 519 MET cc_start: 0.6918 (mmt) cc_final: 0.6675 (mmp) REVERT: E 636 CYS cc_start: 0.8701 (t) cc_final: 0.8116 (p) REVERT: E 646 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.5943 (mm) REVERT: F 1 MET cc_start: 0.4705 (ptm) cc_final: 0.3920 (ptm) REVERT: F 298 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8985 (pp) REVERT: F 393 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6838 (tt) REVERT: F 394 THR cc_start: 0.6740 (OUTLIER) cc_final: 0.6227 (m) REVERT: F 442 LYS cc_start: 0.7366 (tptt) cc_final: 0.6971 (tttt) REVERT: F 541 MET cc_start: 0.8239 (mmt) cc_final: 0.7875 (mmt) REVERT: F 675 MET cc_start: 0.5690 (mtt) cc_final: 0.5458 (ttt) REVERT: F 711 ASP cc_start: 0.7390 (p0) cc_final: 0.7076 (p0) outliers start: 299 outliers final: 195 residues processed: 955 average time/residue: 0.5316 time to fit residues: 891.0354 Evaluate side-chains 908 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 684 time to evaluate : 5.345 ------------------------------------------------------------------------------- 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 276 MET Chi-restraints excluded: chain 2 residue 302 THR Chi-restraints excluded: chain 2 residue 306 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 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 191 LEU Chi-restraints excluded: chain 3 residue 221 LEU Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 386 MET Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 430 ILE Chi-restraints excluded: chain 3 residue 478 MET 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 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 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 551 THR 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 746 PHE Chi-restraints excluded: chain 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 65 MET 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 377 SER Chi-restraints excluded: chain 5 residue 444 SER Chi-restraints excluded: chain 5 residue 478 CYS 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 5 residue 681 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 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 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 695 LEU 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 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 248 VAL Chi-restraints excluded: chain 7 residue 251 VAL Chi-restraints excluded: chain 7 residue 263 ASP 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 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 483 THR 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 7 residue 690 LEU Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain A residue 205 ARG 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 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 628 SER 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 A residue 833 ASP 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 191 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 240 LYS 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 413 THR Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 364 VAL 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 702 PHE Chi-restraints excluded: chain C residue 729 LEU Chi-restraints excluded: chain C residue 746 PHE 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 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 377 SER Chi-restraints excluded: chain D residue 413 LEU 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 D residue 677 VAL 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 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 699 LEU Chi-restraints excluded: chain E residue 700 ASN Chi-restraints excluded: chain E residue 796 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 263 ASP 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 476 ILE Chi-restraints excluded: chain F residue 491 VAL 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 642 ILE Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain F residue 696 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 770 random chunks: chunk 175 optimal weight: 30.0000 chunk 611 optimal weight: 2.9990 chunk 525 optimal weight: 4.9990 chunk 93 optimal weight: 0.0370 chunk 89 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 476 optimal weight: 0.0980 chunk 461 optimal weight: 3.9990 chunk 705 optimal weight: 0.5980 chunk 209 optimal weight: 4.9990 chunk 534 optimal weight: 8.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 51 ASN 3 531 GLN 5 576 HIS 6 669 HIS 6 700 ASN 6 730 HIS B 51 ASN B 351 ASN C 410 GLN E 669 HIS F 544 GLN F 622 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.140368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108603 restraints weight = 122142.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109203 restraints weight = 86843.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.109484 restraints weight = 91465.696| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 63714 Z= 0.183 Angle : 0.711 13.390 86712 Z= 0.361 Chirality : 0.044 0.292 10082 Planarity : 0.004 0.061 10746 Dihedral : 14.471 129.649 9770 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 4.04 % Allowed : 17.74 % Favored : 78.22 % 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: -1.91 (0.10), residues: 7548 helix: 0.72 (0.10), residues: 2656 sheet: -1.84 (0.16), residues: 1084 loop : -2.66 (0.09), residues: 3808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.008 0.001 HIS 7 622 PHE 0.018 0.001 PHE 5 31 TYR 0.015 0.001 TYR 3 327 ARG 0.011 0.000 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 1018 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 751 time to evaluate : 5.336 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: 2 279 THR cc_start: 0.8082 (m) cc_final: 0.7860 (p) REVERT: 2 302 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7816 (t) REVERT: 2 392 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7895 (tm-30) REVERT: 2 501 MET cc_start: 0.7357 (tpp) cc_final: 0.7135 (tpp) REVERT: 2 614 ASP cc_start: 0.8028 (p0) cc_final: 0.7386 (t0) REVERT: 2 781 MET cc_start: 0.7474 (mtt) cc_final: 0.7266 (ptt) REVERT: 3 191 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7992 (mt) REVERT: 3 205 LYS cc_start: 0.7611 (mmmt) cc_final: 0.7313 (tppt) REVERT: 3 234 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6925 (mm-30) REVERT: 3 279 ASP cc_start: 0.7900 (m-30) cc_final: 0.7412 (m-30) REVERT: 3 346 ASP cc_start: 0.7354 (m-30) cc_final: 0.6933 (m-30) REVERT: 3 482 ASP cc_start: 0.8261 (p0) cc_final: 0.7403 (t0) REVERT: 3 535 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8565 (pp) REVERT: 4 206 ARG cc_start: 0.8829 (mmt90) cc_final: 0.8522 (mpt180) REVERT: 4 273 ASP cc_start: 0.8332 (m-30) cc_final: 0.8047 (m-30) REVERT: 4 533 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7343 (pt) REVERT: 4 561 ASP cc_start: 0.6909 (t0) cc_final: 0.6517 (p0) REVERT: 4 702 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8296 (m-10) REVERT: 4 780 MET cc_start: 0.7660 (mmp) cc_final: 0.7194 (mmm) REVERT: 5 65 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.6952 (mtp) REVERT: 5 76 TYR cc_start: 0.8218 (t80) cc_final: 0.7511 (t80) REVERT: 5 218 GLU cc_start: 0.5094 (OUTLIER) cc_final: 0.2694 (mt-10) REVERT: 5 234 LYS cc_start: 0.6864 (pptt) cc_final: 0.6282 (ptpt) REVERT: 5 331 LEU cc_start: 0.7826 (pt) cc_final: 0.7620 (pt) REVERT: 5 454 GLN cc_start: 0.8306 (tt0) cc_final: 0.6991 (tm-30) REVERT: 5 465 GLU cc_start: 0.7875 (tp30) cc_final: 0.6599 (tp30) REVERT: 5 469 MET cc_start: 0.9014 (mmt) cc_final: 0.8736 (mmt) REVERT: 5 513 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8434 (pp) REVERT: 5 661 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7781 (mt-10) REVERT: 5 689 MET cc_start: 0.8411 (mmm) cc_final: 0.8131 (mtt) REVERT: 6 175 TYR cc_start: 0.8516 (t80) cc_final: 0.8196 (t80) REVERT: 6 379 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8730 (m) REVERT: 6 519 MET cc_start: 0.6971 (mmt) cc_final: 0.6726 (mmp) REVERT: 6 525 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8080 (pt) REVERT: 6 636 CYS cc_start: 0.8595 (t) cc_final: 0.7874 (p) REVERT: 6 646 ILE cc_start: 0.6832 (OUTLIER) cc_final: 0.6431 (tt) REVERT: 6 805 ARG cc_start: 0.8017 (ptp-170) cc_final: 0.7801 (mtt180) REVERT: 7 298 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8998 (pp) REVERT: 7 394 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6556 (m) REVERT: 7 402 MET cc_start: 0.8193 (tpp) cc_final: 0.7804 (tpp) REVERT: A 279 THR cc_start: 0.8085 (m) cc_final: 0.7876 (p) REVERT: A 302 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7657 (t) REVERT: A 781 MET cc_start: 0.7886 (mtt) cc_final: 0.7235 (ptt) REVERT: B 191 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8046 (mt) REVERT: B 234 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6879 (mm-30) REVERT: B 240 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8468 (mmmm) REVERT: B 279 ASP cc_start: 0.7975 (m-30) cc_final: 0.7531 (m-30) REVERT: B 346 ASP cc_start: 0.7339 (m-30) cc_final: 0.7032 (m-30) REVERT: B 443 THR cc_start: 0.8860 (p) cc_final: 0.8569 (t) REVERT: B 490 MET cc_start: 0.8829 (tpp) cc_final: 0.8510 (tpp) REVERT: C 273 ASP cc_start: 0.8242 (m-30) cc_final: 0.7930 (m-30) REVERT: C 561 ASP cc_start: 0.7036 (t0) cc_final: 0.6503 (p0) REVERT: C 702 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8225 (m-10) REVERT: C 780 MET cc_start: 0.7568 (mmp) cc_final: 0.7016 (mmm) REVERT: D 65 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7005 (mtp) REVERT: D 76 TYR cc_start: 0.8151 (t80) cc_final: 0.7478 (t80) REVERT: D 218 GLU cc_start: 0.5069 (OUTLIER) cc_final: 0.2364 (mt-10) REVERT: D 234 LYS cc_start: 0.6886 (pptt) cc_final: 0.6376 (ptmt) REVERT: D 454 GLN cc_start: 0.8324 (tt0) cc_final: 0.7693 (tm-30) REVERT: D 456 ASP cc_start: 0.6405 (t0) cc_final: 0.6073 (t0) REVERT: D 465 GLU cc_start: 0.7586 (tp30) cc_final: 0.7228 (mm-30) REVERT: D 469 MET cc_start: 0.9079 (mmt) cc_final: 0.8834 (mmt) REVERT: D 513 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8629 (pp) REVERT: D 689 MET cc_start: 0.7471 (mtt) cc_final: 0.7039 (mmp) REVERT: E 175 TYR cc_start: 0.8456 (t80) cc_final: 0.8154 (t80) REVERT: E 261 ARG cc_start: 0.4093 (mpt180) cc_final: 0.3528 (mtt90) REVERT: E 379 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8723 (m) REVERT: E 519 MET cc_start: 0.6890 (mmt) cc_final: 0.6673 (mmp) REVERT: E 636 CYS cc_start: 0.8702 (t) cc_final: 0.8006 (p) REVERT: F 1 MET cc_start: 0.4664 (ptm) cc_final: 0.3941 (ptm) REVERT: F 84 ASP cc_start: 0.8206 (m-30) cc_final: 0.8002 (m-30) REVERT: F 298 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8974 (pp) REVERT: F 393 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7022 (tt) REVERT: F 394 THR cc_start: 0.6736 (OUTLIER) cc_final: 0.6361 (m) REVERT: F 402 MET cc_start: 0.7933 (mmm) cc_final: 0.7687 (mmm) REVERT: F 442 LYS cc_start: 0.7323 (tptt) cc_final: 0.6963 (ttmt) REVERT: F 541 MET cc_start: 0.8263 (mmt) cc_final: 0.7937 (mmt) REVERT: F 711 ASP cc_start: 0.7403 (p0) cc_final: 0.7050 (p0) outliers start: 267 outliers final: 174 residues processed: 955 average time/residue: 0.5333 time to fit residues: 896.7673 Evaluate side-chains 897 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 699 time to evaluate : 5.290 ------------------------------------------------------------------------------- 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 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 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 191 LEU Chi-restraints excluded: chain 3 residue 257 THR Chi-restraints excluded: chain 3 residue 413 THR Chi-restraints excluded: chain 3 residue 430 ILE Chi-restraints excluded: chain 3 residue 478 MET 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 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 564 ILE Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 605 ILE Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 65 MET 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 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 513 LEU Chi-restraints excluded: chain 5 residue 575 ILE Chi-restraints excluded: chain 5 residue 576 HIS 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 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 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 695 LEU Chi-restraints excluded: chain 6 residue 699 LEU Chi-restraints excluded: chain 6 residue 700 ASN 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 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 331 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 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 642 ILE Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain A residue 205 ARG 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 628 SER Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 806 THR 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 191 LEU Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 364 VAL 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 564 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 702 PHE Chi-restraints excluded: chain C residue 746 PHE 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 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 377 SER Chi-restraints excluded: chain D residue 430 GLU 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 648 ILE Chi-restraints excluded: chain D residue 677 VAL 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 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 699 LEU Chi-restraints excluded: chain E residue 700 ASN Chi-restraints excluded: chain E residue 751 LEU Chi-restraints excluded: chain E residue 766 THR Chi-restraints excluded: chain E residue 796 THR 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 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 331 LEU 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 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 601 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 287 optimal weight: 4.9990 chunk 724 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 342 optimal weight: 0.0010 chunk 93 optimal weight: 0.0670 chunk 36 optimal weight: 0.1980 chunk 569 optimal weight: 5.9990 chunk 545 optimal weight: 9.9990 chunk 557 optimal weight: 7.9990 chunk 414 optimal weight: 20.0000 chunk 469 optimal weight: 0.0020 overall best weight: 1.0534 ------------------------------------------------------------------------------- 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 ** 3 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 253 GLN 5 514 ASN 5 576 HIS 6 669 HIS 6 700 ASN 7 68 GLN 7 622 HIS B 51 ASN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 669 HIS E 690 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110325 restraints weight = 122434.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110505 restraints weight = 90531.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.111082 restraints weight = 92852.855| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4638 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= 0.174 Angle : 0.714 13.372 86712 Z= 0.359 Chirality : 0.044 0.296 10082 Planarity : 0.004 0.065 10746 Dihedral : 14.327 131.218 9765 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.97 % Favored : 91.00 % Rotamer: Outliers : 3.78 % Allowed : 18.45 % Favored : 77.77 % 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: -1.73 (0.10), residues: 7548 helix: 0.83 (0.10), residues: 2674 sheet: -1.66 (0.16), residues: 1078 loop : -2.57 (0.09), residues: 3796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 476 HIS 0.021 0.001 HIS 5 576 PHE 0.017 0.001 PHE D 31 TYR 0.014 0.001 TYR B 211 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 1009 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 759 time to evaluate : 5.252 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: 2 255 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8295 (tt) REVERT: 2 279 THR cc_start: 0.7972 (m) cc_final: 0.7744 (p) REVERT: 2 302 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7492 (p) REVERT: 2 614 ASP cc_start: 0.7941 (p0) cc_final: 0.7276 (t0) REVERT: 3 234 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6874 (mm-30) REVERT: 3 279 ASP cc_start: 0.7805 (m-30) cc_final: 0.7309 (m-30) REVERT: 3 346 ASP cc_start: 0.7358 (m-30) cc_final: 0.6929 (m-30) REVERT: 3 482 ASP cc_start: 0.8210 (p0) cc_final: 0.7354 (t0) REVERT: 3 535 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8553 (pp) REVERT: 4 206 ARG cc_start: 0.8738 (mmt90) cc_final: 0.8484 (mpt180) REVERT: 4 273 ASP cc_start: 0.8184 (m-30) cc_final: 0.7898 (m-30) REVERT: 4 533 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7270 (pt) REVERT: 4 561 ASP cc_start: 0.6819 (t0) cc_final: 0.6449 (p0) REVERT: 4 780 MET cc_start: 0.7634 (mmp) cc_final: 0.7162 (mmm) REVERT: 5 65 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.6968 (mtp) REVERT: 5 76 TYR cc_start: 0.8169 (t80) cc_final: 0.7472 (t80) REVERT: 5 234 LYS cc_start: 0.7069 (pptt) cc_final: 0.6581 (ptpt) REVERT: 5 404 MET cc_start: 0.7954 (ppp) cc_final: 0.7749 (ppp) REVERT: 5 454 GLN cc_start: 0.8181 (tt0) cc_final: 0.7557 (tm-30) REVERT: 5 465 GLU cc_start: 0.7869 (tp30) cc_final: 0.7409 (mm-30) REVERT: 5 469 MET cc_start: 0.8973 (mmt) cc_final: 0.8755 (mmt) REVERT: 5 513 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8506 (pp) REVERT: 5 661 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7765 (mt-10) REVERT: 5 689 MET cc_start: 0.8355 (mmm) cc_final: 0.8104 (mtt) REVERT: 6 175 TYR cc_start: 0.8405 (t80) cc_final: 0.8097 (t80) REVERT: 6 379 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8713 (m) REVERT: 6 519 MET cc_start: 0.6907 (mmt) cc_final: 0.6658 (mmp) REVERT: 6 525 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8151 (pt) REVERT: 6 540 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6704 (p90) REVERT: 6 646 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6435 (tt) REVERT: 6 678 ILE cc_start: 0.9386 (mp) cc_final: 0.9071 (mm) REVERT: 7 298 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8980 (pp) REVERT: 7 394 THR cc_start: 0.6710 (OUTLIER) cc_final: 0.6396 (m) REVERT: 7 443 ARG cc_start: 0.7717 (tmm-80) cc_final: 0.7363 (tmm-80) REVERT: A 255 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8362 (tt) REVERT: A 279 THR cc_start: 0.7987 (m) cc_final: 0.7774 (p) REVERT: A 302 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7668 (t) REVERT: A 781 MET cc_start: 0.7750 (mtt) cc_final: 0.7134 (ptt) REVERT: B 191 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.8006 (mt) REVERT: B 205 LYS cc_start: 0.7516 (mmmt) cc_final: 0.7194 (tppt) REVERT: B 234 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6828 (mm-30) REVERT: B 279 ASP cc_start: 0.7791 (m-30) cc_final: 0.7350 (m-30) REVERT: B 346 ASP cc_start: 0.7255 (m-30) cc_final: 0.6943 (m-30) REVERT: B 443 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8574 (t) REVERT: B 482 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7201 (m-30) REVERT: C 273 ASP cc_start: 0.8176 (m-30) cc_final: 0.7877 (m-30) REVERT: C 561 ASP cc_start: 0.6939 (t0) cc_final: 0.6453 (p0) REVERT: C 728 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7587 (t80) REVERT: C 780 MET cc_start: 0.7596 (mmp) cc_final: 0.7024 (mmm) REVERT: D 65 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7030 (mtp) REVERT: D 76 TYR cc_start: 0.8139 (t80) cc_final: 0.7474 (t80) REVERT: D 234 LYS cc_start: 0.6850 (pptt) cc_final: 0.6237 (ptpt) REVERT: D 454 GLN cc_start: 0.8117 (tt0) cc_final: 0.7751 (tm-30) REVERT: D 456 ASP cc_start: 0.6526 (t0) cc_final: 0.6186 (t0) REVERT: D 465 GLU cc_start: 0.7578 (tp30) cc_final: 0.7341 (mm-30) REVERT: D 469 MET cc_start: 0.8987 (mmt) cc_final: 0.8764 (mmt) REVERT: D 513 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8583 (pp) REVERT: D 676 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7429 (t-170) REVERT: D 689 MET cc_start: 0.7452 (mtt) cc_final: 0.6953 (mmp) REVERT: E 175 TYR cc_start: 0.8390 (t80) cc_final: 0.8102 (t80) REVERT: E 261 ARG cc_start: 0.4120 (mpt180) cc_final: 0.3281 (mtt90) REVERT: E 379 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8706 (m) REVERT: E 527 ASP cc_start: 0.8591 (t0) cc_final: 0.8309 (t70) REVERT: E 636 CYS cc_start: 0.8684 (t) cc_final: 0.8084 (p) REVERT: E 646 ILE cc_start: 0.6449 (OUTLIER) cc_final: 0.6008 (mm) REVERT: F 84 ASP cc_start: 0.8149 (m-30) cc_final: 0.7945 (m-30) REVERT: F 298 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8955 (pp) REVERT: F 393 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7053 (tt) REVERT: F 394 THR cc_start: 0.6572 (OUTLIER) cc_final: 0.6157 (m) REVERT: F 541 MET cc_start: 0.8312 (mmt) cc_final: 0.8031 (mmt) REVERT: F 711 ASP cc_start: 0.7338 (p0) cc_final: 0.6980 (p0) outliers start: 250 outliers final: 170 residues processed: 949 average time/residue: 0.5741 time to fit residues: 962.3992 Evaluate side-chains 899 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 703 time to evaluate : 5.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 257 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 430 ILE 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 389 CYS Chi-restraints excluded: chain 4 residue 417 LEU Chi-restraints excluded: chain 4 residue 442 ILE 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 564 ILE Chi-restraints excluded: chain 4 residue 596 SER Chi-restraints excluded: chain 4 residue 605 ILE Chi-restraints excluded: chain 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 65 MET 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 236 CYS Chi-restraints excluded: chain 5 residue 264 LEU Chi-restraints excluded: chain 5 residue 405 ARG Chi-restraints excluded: chain 5 residue 444 SER Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 576 HIS 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 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 646 ILE Chi-restraints excluded: chain 6 residue 695 LEU Chi-restraints excluded: chain 6 residue 700 ASN Chi-restraints excluded: chain 6 residue 751 LEU Chi-restraints excluded: chain 7 residue 25 LEU Chi-restraints excluded: chain 7 residue 83 ASP 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 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 483 THR Chi-restraints excluded: chain 7 residue 491 VAL Chi-restraints excluded: chain 7 residue 497 VAL Chi-restraints excluded: chain 7 residue 507 ILE 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 7 residue 696 SER Chi-restraints excluded: chain A residue 226 VAL 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 347 ILE Chi-restraints excluded: chain A residue 402 LEU 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 628 SER 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 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 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 191 LEU 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 443 THR 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 364 VAL 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 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 634 PHE Chi-restraints excluded: chain C residue 728 TYR Chi-restraints excluded: chain C residue 801 MET 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 603 ILE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain D residue 677 VAL 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 641 PHE Chi-restraints excluded: chain E residue 646 ILE Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain E residue 700 ASN Chi-restraints excluded: chain E residue 766 THR Chi-restraints excluded: chain E residue 796 THR Chi-restraints excluded: chain F residue 83 ASP 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 331 LEU 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 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 578 LEU 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 398 optimal weight: 5.9990 chunk 618 optimal weight: 5.9990 chunk 666 optimal weight: 7.9990 chunk 566 optimal weight: 5.9990 chunk 554 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 590 optimal weight: 3.9990 chunk 546 optimal weight: 1.9990 chunk 516 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 51 ASN ** 3 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 253 GLN 6 669 HIS A 202 ASN A 340 ASN B 51 ASN C 651 GLN E 669 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.139602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107799 restraints weight = 122271.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.108376 restraints weight = 83947.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.108496 restraints weight = 97918.039| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4736 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= 0.225 Angle : 0.738 13.755 86712 Z= 0.370 Chirality : 0.045 0.413 10082 Planarity : 0.005 0.064 10746 Dihedral : 14.302 131.952 9762 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 3.80 % Allowed : 19.17 % Favored : 77.03 % 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: -1.66 (0.10), residues: 7548 helix: 0.94 (0.10), residues: 2662 sheet: -1.64 (0.16), residues: 1092 loop : -2.55 (0.09), residues: 3794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.009 0.001 HIS 5 576 PHE 0.021 0.001 PHE 5 31 TYR 0.027 0.001 TYR B 211 ARG 0.015 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 972 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 721 time to evaluate : 5.401 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: 0.8090 (m) cc_final: 0.7844 (p) REVERT: 2 302 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7777 (t) REVERT: 2 390 LEU cc_start: 0.9061 (tt) cc_final: 0.8839 (tp) REVERT: 2 392 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7911 (tm-30) REVERT: 2 614 ASP cc_start: 0.7990 (p0) cc_final: 0.7280 (t0) REVERT: 3 205 LYS cc_start: 0.7687 (mmmt) cc_final: 0.7268 (tppt) REVERT: 3 234 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6945 (mm-30) REVERT: 3 279 ASP cc_start: 0.7847 (m-30) cc_final: 0.7370 (m-30) REVERT: 3 346 ASP cc_start: 0.7361 (m-30) cc_final: 0.6944 (m-30) REVERT: 3 482 ASP cc_start: 0.8288 (p0) cc_final: 0.7439 (t0) REVERT: 3 535 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8575 (pp) REVERT: 4 206 ARG cc_start: 0.8786 (mmt90) cc_final: 0.8501 (mpt180) REVERT: 4 273 ASP cc_start: 0.8263 (m-30) cc_final: 0.7979 (m-30) REVERT: 4 533 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7362 (pt) REVERT: 4 561 ASP cc_start: 0.6849 (t0) cc_final: 0.6466 (p0) REVERT: 4 637 MET cc_start: 0.8304 (mmm) cc_final: 0.7745 (ttp) REVERT: 4 702 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8304 (m-10) REVERT: 4 780 MET cc_start: 0.7723 (mmp) cc_final: 0.7249 (mmm) REVERT: 5 65 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7253 (mtp) REVERT: 5 76 TYR cc_start: 0.8321 (t80) cc_final: 0.7666 (t80) REVERT: 5 218 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.2554 (mt-10) REVERT: 5 234 LYS cc_start: 0.6965 (pptt) cc_final: 0.6421 (ptpt) REVERT: 5 331 LEU cc_start: 0.8094 (pt) cc_final: 0.7781 (pp) REVERT: 5 404 MET cc_start: 0.8009 (ppp) cc_final: 0.7743 (ppp) REVERT: 5 454 GLN cc_start: 0.8137 (tt0) cc_final: 0.7352 (tm-30) REVERT: 5 465 GLU cc_start: 0.7873 (tp30) cc_final: 0.7227 (mm-30) REVERT: 5 469 MET cc_start: 0.9071 (mmt) cc_final: 0.8805 (mmt) REVERT: 5 513 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8554 (pp) REVERT: 5 577 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7785 (m) REVERT: 5 661 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7866 (mt-10) REVERT: 5 689 MET cc_start: 0.8460 (mmm) cc_final: 0.8080 (mtt) REVERT: 6 175 TYR cc_start: 0.8579 (t80) cc_final: 0.8308 (t80) REVERT: 6 296 ARG cc_start: 0.7539 (ttm170) cc_final: 0.6900 (ttm-80) REVERT: 6 379 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8728 (m) REVERT: 6 519 MET cc_start: 0.6985 (mmt) cc_final: 0.6754 (mmp) REVERT: 6 540 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.6742 (p90) REVERT: 6 646 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6432 (tt) REVERT: 6 678 ILE cc_start: 0.9377 (mp) cc_final: 0.8873 (mm) REVERT: 7 298 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9043 (pp) REVERT: 7 394 THR cc_start: 0.6711 (OUTLIER) cc_final: 0.6399 (m) REVERT: 7 443 ARG cc_start: 0.7784 (tmm-80) cc_final: 0.7422 (tmm-80) REVERT: 7 529 MET cc_start: 0.8571 (mmt) cc_final: 0.8034 (mmt) REVERT: 7 602 ASP cc_start: 0.6909 (t0) cc_final: 0.6466 (p0) REVERT: A 279 THR cc_start: 0.8041 (m) cc_final: 0.7820 (p) REVERT: A 302 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7660 (t) REVERT: A 781 MET cc_start: 0.7839 (mtt) cc_final: 0.7217 (ptt) REVERT: B 191 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 205 LYS cc_start: 0.7566 (mmmt) cc_final: 0.7286 (tppt) REVERT: B 234 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6882 (mm-30) REVERT: B 279 ASP cc_start: 0.7889 (m-30) cc_final: 0.7440 (m-30) REVERT: B 346 ASP cc_start: 0.7255 (m-30) cc_final: 0.6946 (m-30) REVERT: B 482 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: C 273 ASP cc_start: 0.8282 (m-30) cc_final: 0.8000 (m-30) REVERT: C 561 ASP cc_start: 0.6907 (t0) cc_final: 0.6431 (p0) REVERT: C 702 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: C 780 MET cc_start: 0.7674 (mmp) cc_final: 0.7108 (mmm) REVERT: D 65 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7262 (mtp) REVERT: D 76 TYR cc_start: 0.8219 (t80) cc_final: 0.7571 (t80) REVERT: D 234 LYS cc_start: 0.6889 (pptt) cc_final: 0.6340 (ptpt) REVERT: D 456 ASP cc_start: 0.6534 (t0) cc_final: 0.6264 (t0) REVERT: D 469 MET cc_start: 0.9070 (mmt) cc_final: 0.8822 (mmt) REVERT: D 513 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8599 (pp) REVERT: D 676 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7496 (t-170) REVERT: D 689 MET cc_start: 0.7583 (mtt) cc_final: 0.6972 (mmp) REVERT: E 175 TYR cc_start: 0.8539 (t80) cc_final: 0.8219 (t80) REVERT: E 261 ARG cc_start: 0.4145 (mpt180) cc_final: 0.3500 (mtt90) REVERT: E 379 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8707 (m) REVERT: E 519 MET cc_start: 0.7068 (mmp) cc_final: 0.6783 (ptp) REVERT: E 636 CYS cc_start: 0.8733 (t) cc_final: 0.7978 (p) REVERT: E 646 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6246 (mm) REVERT: F 298 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9024 (pp) REVERT: F 393 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7073 (tt) REVERT: F 394 THR cc_start: 0.6642 (OUTLIER) cc_final: 0.6202 (m) REVERT: F 402 MET cc_start: 0.8004 (mmm) cc_final: 0.7748 (mmm) REVERT: F 443 ARG cc_start: 0.7727 (tmm-80) cc_final: 0.7180 (tmm-80) REVERT: F 541 MET cc_start: 0.8295 (mmt) cc_final: 0.8039 (mmt) REVERT: F 602 ASP cc_start: 0.7098 (t0) cc_final: 0.6582 (p0) REVERT: F 711 ASP cc_start: 0.7508 (p0) cc_final: 0.7150 (p0) outliers start: 251 outliers final: 193 residues processed: 907 average time/residue: 0.5195 time to fit residues: 831.5281 Evaluate side-chains 911 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 693 time to evaluate : 5.313 ------------------------------------------------------------------------------- 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 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 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 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 292 VAL 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 224 LEU Chi-restraints excluded: chain 4 residue 249 LEU 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 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 605 ILE Chi-restraints excluded: chain 4 residue 616 LEU Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 4 residue 712 VAL Chi-restraints excluded: chain 4 residue 746 PHE Chi-restraints excluded: chain 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 50 LEU Chi-restraints excluded: chain 5 residue 65 MET 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 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 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 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 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 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 646 ILE Chi-restraints excluded: chain 6 residue 695 LEU Chi-restraints excluded: chain 6 residue 700 ASN Chi-restraints excluded: chain 6 residue 751 LEU Chi-restraints excluded: chain 6 residue 819 ILE Chi-restraints excluded: chain 7 residue 83 ASP 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 300 MET Chi-restraints excluded: chain 7 residue 315 ILE Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 331 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 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 621 MET Chi-restraints excluded: chain 7 residue 642 ILE 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 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 519 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 628 SER 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 191 LEU Chi-restraints excluded: chain B residue 221 LEU 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 443 THR 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 271 ILE 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 451 ARG 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 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 634 PHE Chi-restraints excluded: chain C residue 702 PHE Chi-restraints excluded: chain C residue 746 PHE Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain D residue 27 ILE 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 349 PHE 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 444 SER Chi-restraints excluded: chain D residue 453 VAL 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 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 700 ASN Chi-restraints excluded: chain E residue 766 THR Chi-restraints excluded: chain E residue 796 THR Chi-restraints excluded: chain E residue 797 VAL Chi-restraints excluded: chain F residue 83 ASP 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 331 LEU 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 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 578 LEU Chi-restraints excluded: chain F residue 601 LEU 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 717 optimal weight: 4.9990 chunk 716 optimal weight: 1.9990 chunk 321 optimal weight: 5.9990 chunk 384 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 534 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 311 optimal weight: 0.4980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 ** 3 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS B 51 ASN C 808 HIS E 669 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.139533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107697 restraints weight = 122028.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108740 restraints weight = 86323.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.108885 restraints weight = 92041.356| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4855 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= 0.219 Angle : 0.741 12.415 86712 Z= 0.372 Chirality : 0.045 0.342 10082 Planarity : 0.005 0.064 10746 Dihedral : 14.253 130.565 9762 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.84 % Favored : 90.13 % Rotamer: Outliers : 3.60 % Allowed : 19.52 % Favored : 76.88 % 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: -1.56 (0.10), residues: 7548 helix: 1.01 (0.10), residues: 2650 sheet: -1.54 (0.16), residues: 1084 loop : -2.48 (0.09), residues: 3814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.005 0.001 HIS 3 164 PHE 0.024 0.001 PHE D 31 TYR 0.022 0.001 TYR B 211 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 964 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 726 time to evaluate : 5.373 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: 2 255 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8268 (tt) REVERT: 2 279 THR cc_start: 0.7998 (m) cc_final: 0.7770 (p) REVERT: 2 302 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7731 (t) REVERT: 2 390 LEU cc_start: 0.9021 (tt) cc_final: 0.8801 (tp) REVERT: 2 392 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7796 (tm-30) REVERT: 2 614 ASP cc_start: 0.7912 (p0) cc_final: 0.7257 (t0) REVERT: 3 205 LYS cc_start: 0.7576 (mmmt) cc_final: 0.7185 (tppt) REVERT: 3 234 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6913 (mm-30) REVERT: 3 279 ASP cc_start: 0.7875 (m-30) cc_final: 0.7371 (m-30) REVERT: 3 346 ASP cc_start: 0.7370 (m-30) cc_final: 0.6951 (m-30) REVERT: 3 482 ASP cc_start: 0.8248 (p0) cc_final: 0.7383 (t0) REVERT: 3 535 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8592 (pp) REVERT: 4 206 ARG cc_start: 0.8767 (mmt90) cc_final: 0.8482 (mpt180) REVERT: 4 273 ASP cc_start: 0.8273 (m-30) cc_final: 0.7990 (m-30) REVERT: 4 561 ASP cc_start: 0.6795 (t0) cc_final: 0.6399 (p0) REVERT: 4 702 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8289 (m-10) REVERT: 4 780 MET cc_start: 0.7620 (mmp) cc_final: 0.7188 (mmm) REVERT: 5 65 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7162 (mtp) REVERT: 5 76 TYR cc_start: 0.8309 (t80) cc_final: 0.7655 (t80) REVERT: 5 234 LYS cc_start: 0.7014 (pptt) cc_final: 0.6448 (ptpt) REVERT: 5 331 LEU cc_start: 0.8108 (pt) cc_final: 0.7852 (pp) REVERT: 5 465 GLU cc_start: 0.7861 (tp30) cc_final: 0.7436 (mm-30) REVERT: 5 469 MET cc_start: 0.9071 (mmt) cc_final: 0.8822 (mmt) REVERT: 5 513 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8482 (pp) REVERT: 5 661 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7859 (mt-10) REVERT: 5 676 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7278 (t-170) REVERT: 5 689 MET cc_start: 0.8337 (mmm) cc_final: 0.7942 (mtt) REVERT: 6 175 TYR cc_start: 0.8536 (t80) cc_final: 0.8204 (t80) REVERT: 6 379 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8733 (m) REVERT: 6 519 MET cc_start: 0.6938 (mmt) cc_final: 0.6718 (mmp) REVERT: 6 540 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.6714 (p90) REVERT: 6 646 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6466 (tt) REVERT: 6 678 ILE cc_start: 0.9385 (mp) cc_final: 0.9135 (mm) REVERT: 7 298 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9030 (pp) REVERT: 7 394 THR cc_start: 0.6646 (OUTLIER) cc_final: 0.6306 (m) REVERT: 7 402 MET cc_start: 0.7872 (mmm) cc_final: 0.7246 (mmm) REVERT: 7 443 ARG cc_start: 0.7680 (tmm-80) cc_final: 0.7296 (tmm-80) REVERT: A 279 THR cc_start: 0.8000 (m) cc_final: 0.7786 (p) REVERT: A 302 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7649 (t) REVERT: A 781 MET cc_start: 0.7794 (mtt) cc_final: 0.7249 (ptt) REVERT: B 191 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8084 (mt) REVERT: B 205 LYS cc_start: 0.7533 (mmmt) cc_final: 0.7304 (tppt) REVERT: B 234 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6899 (mm-30) REVERT: B 261 MET cc_start: 0.8594 (ptt) cc_final: 0.8360 (ptt) REVERT: B 279 ASP cc_start: 0.7824 (m-30) cc_final: 0.7357 (m-30) REVERT: B 346 ASP cc_start: 0.7280 (m-30) cc_final: 0.6956 (m-30) REVERT: B 482 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: C 273 ASP cc_start: 0.8274 (m-30) cc_final: 0.7983 (m-30) REVERT: C 401 GLU cc_start: 0.8582 (pm20) cc_final: 0.8245 (pm20) REVERT: C 561 ASP cc_start: 0.6819 (t0) cc_final: 0.6372 (p0) REVERT: C 702 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8272 (m-10) REVERT: C 780 MET cc_start: 0.7576 (mmp) cc_final: 0.7024 (mmm) REVERT: D 65 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7331 (mtp) REVERT: D 76 TYR cc_start: 0.8202 (t80) cc_final: 0.7651 (t80) REVERT: D 234 LYS cc_start: 0.6892 (pptt) cc_final: 0.6360 (ptpt) REVERT: D 454 GLN cc_start: 0.8224 (tt0) cc_final: 0.7912 (tt0) REVERT: D 456 ASP cc_start: 0.6520 (t0) cc_final: 0.6271 (t0) REVERT: D 469 MET cc_start: 0.9049 (mmt) cc_final: 0.8772 (mmt) REVERT: D 481 GLU cc_start: 0.8706 (tp30) cc_final: 0.8040 (tm-30) REVERT: D 484 LYS cc_start: 0.8859 (tptp) cc_final: 0.7733 (tptp) REVERT: D 513 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8564 (pp) REVERT: D 676 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7480 (t-170) REVERT: D 689 MET cc_start: 0.7571 (mtt) cc_final: 0.6969 (mmp) REVERT: E 175 TYR cc_start: 0.8504 (t80) cc_final: 0.8190 (t80) REVERT: E 261 ARG cc_start: 0.3966 (mpt180) cc_final: 0.3365 (mtt90) REVERT: E 379 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8725 (m) REVERT: E 519 MET cc_start: 0.7128 (mmp) cc_final: 0.6894 (ptp) REVERT: E 636 CYS cc_start: 0.8711 (t) cc_final: 0.7969 (p) REVERT: E 646 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6239 (mm) REVERT: F 298 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9017 (pp) REVERT: F 393 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7013 (tt) REVERT: F 394 THR cc_start: 0.6548 (OUTLIER) cc_final: 0.6111 (m) REVERT: F 443 ARG cc_start: 0.7688 (tmm-80) cc_final: 0.7220 (tmm-80) REVERT: F 541 MET cc_start: 0.8291 (mmt) cc_final: 0.8053 (mmt) REVERT: F 602 ASP cc_start: 0.6971 (t0) cc_final: 0.6567 (p0) REVERT: F 711 ASP cc_start: 0.7465 (p0) cc_final: 0.7079 (p0) outliers start: 238 outliers final: 185 residues processed: 906 average time/residue: 0.5317 time to fit residues: 851.7567 Evaluate side-chains 900 residues out of total 6746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 691 time to evaluate : 5.292 ------------------------------------------------------------------------------- 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 539 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 260 GLU Chi-restraints excluded: chain 3 residue 292 VAL 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 389 CYS 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 474 LEU Chi-restraints excluded: chain 4 residue 492 HIS Chi-restraints excluded: chain 4 residue 522 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 605 ILE Chi-restraints excluded: chain 4 residue 616 LEU Chi-restraints excluded: chain 4 residue 702 PHE Chi-restraints excluded: chain 4 residue 746 PHE Chi-restraints excluded: chain 4 residue 801 MET Chi-restraints excluded: chain 5 residue 26 GLU Chi-restraints excluded: chain 5 residue 40 LEU Chi-restraints excluded: chain 5 residue 50 LEU Chi-restraints excluded: chain 5 residue 65 MET 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 405 ARG 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 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 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 613 VAL 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 751 LEU Chi-restraints excluded: chain 7 residue 83 ASP Chi-restraints excluded: chain 7 residue 158 THR 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 300 MET Chi-restraints excluded: chain 7 residue 327 ILE Chi-restraints excluded: chain 7 residue 331 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 476 ILE Chi-restraints excluded: chain 7 residue 483 THR 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 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 191 LEU 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 443 THR 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 271 ILE Chi-restraints excluded: chain C residue 364 VAL 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 444 ILE Chi-restraints excluded: chain C residue 451 ARG 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 572 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 634 PHE Chi-restraints excluded: chain C residue 702 PHE Chi-restraints excluded: chain C residue 746 PHE Chi-restraints excluded: chain C residue 801 MET 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 349 PHE 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 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 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 700 ASN Chi-restraints excluded: chain E residue 766 THR Chi-restraints excluded: chain E residue 796 THR Chi-restraints excluded: chain E residue 797 VAL Chi-restraints excluded: chain F residue 83 ASP 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 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0908 > 50: distance: 30 - 35: 7.591 distance: 35 - 36: 20.480 distance: 36 - 37: 20.979 distance: 37 - 38: 5.580 distance: 37 - 39: 42.992 distance: 39 - 40: 12.156 distance: 40 - 41: 23.023 distance: 41 - 42: 12.547 distance: 41 - 47: 63.170 distance: 43 - 44: 42.833 distance: 44 - 45: 4.282 distance: 47 - 48: 40.319 distance: 47 - 53: 39.535 distance: 48 - 49: 15.472 distance: 48 - 51: 4.049 distance: 49 - 50: 44.061 distance: 49 - 54: 41.519 distance: 51 - 52: 35.447 distance: 52 - 53: 31.700 distance: 54 - 55: 24.877 distance: 55 - 56: 33.121 distance: 56 - 57: 18.291 distance: 56 - 58: 39.440 distance: 58 - 59: 9.438 distance: 59 - 60: 12.247 distance: 59 - 62: 21.463 distance: 60 - 61: 7.457 distance: 60 - 65: 41.673 distance: 62 - 63: 16.581 distance: 62 - 64: 29.012 distance: 65 - 66: 15.454 distance: 66 - 67: 22.308 distance: 66 - 69: 8.948 distance: 67 - 68: 4.955 distance: 67 - 70: 19.191 distance: 70 - 71: 7.314 distance: 71 - 72: 13.213 distance: 71 - 74: 23.397 distance: 72 - 73: 13.068 distance: 72 - 79: 12.794 distance: 73 - 102: 6.693 distance: 74 - 75: 13.944 distance: 75 - 76: 21.290 distance: 76 - 77: 8.216 distance: 77 - 78: 21.333 distance: 79 - 80: 13.394 distance: 80 - 81: 11.289 distance: 80 - 83: 4.957 distance: 81 - 82: 25.501 distance: 81 - 85: 27.220 distance: 82 - 110: 29.143 distance: 83 - 84: 21.197 distance: 85 - 86: 14.491 distance: 86 - 87: 16.416 distance: 86 - 89: 13.553 distance: 87 - 88: 11.869 distance: 87 - 94: 4.174 distance: 88 - 116: 11.395 distance: 89 - 90: 4.895 distance: 90 - 91: 25.310 distance: 91 - 92: 11.687 distance: 91 - 93: 24.114 distance: 94 - 95: 5.796 distance: 95 - 96: 7.955 distance: 95 - 98: 20.843 distance: 96 - 97: 10.303 distance: 96 - 102: 9.251 distance: 97 - 120: 16.885 distance: 99 - 100: 9.529 distance: 99 - 101: 13.836