Starting phenix.real_space_refine on Mon Feb 19 05:34:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sac_24948/02_2024/7sac_24948_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sac_24948/02_2024/7sac_24948.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sac_24948/02_2024/7sac_24948_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sac_24948/02_2024/7sac_24948_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sac_24948/02_2024/7sac_24948_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sac_24948/02_2024/7sac_24948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sac_24948/02_2024/7sac_24948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sac_24948/02_2024/7sac_24948_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sac_24948/02_2024/7sac_24948_updated.pdb" } resolution = 3.69 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= 0.004 sd= 0.352 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 298 atoms to isotropic. 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 S 124 5.16 5 Cl 3 4.86 5 C 15067 2.51 5 N 3872 2.21 5 O 4408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A GLU 786": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "B GLU 788": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C GLU 522": "OE1" <-> "OE2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C GLU 698": "OE1" <-> "OE2" Residue "C GLU 739": "OE1" <-> "OE2" Residue "C GLU 786": "OE1" <-> "OE2" Residue "C PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D GLU 500": "OE1" <-> "OE2" Residue "D PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23474 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5888 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 410 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 353 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 17, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 286 Chain: "B" Number of atoms: 5747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5747 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 582 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 17, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 6, 'GLU:plan': 25, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 333 Chain: "C" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5870 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 295 Chain: "D" Number of atoms: 5709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5709 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 17, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 28, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 362 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 72 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 3, 40 Unusual residues: {'JC9': 1, 'NAG': 1} Inner-chain residues flagged as termini: ['pdbres="GLU B 902 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 3, 40 Unusual residues: {'JC9': 1, 'NAG': 1} Inner-chain residues flagged as termini: ['pdbres="GLU B 902 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 23 Conformer: "C" Number of residues, atoms: 3, 40 Unusual residues: {'JC9': 1, 'NAG': 1} Inner-chain residues flagged as termini: ['pdbres="GLU B 902 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 23 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 AJC9 B 903 " occ=0.33 ... (46 atoms not shown) pdb="CL1 CJC9 B 903 " occ=0.33 Time building chain proxies: 12.81, per 1000 atoms: 0.55 Number of scatterers: 23474 At special positions: 0 Unit cell: (124.976, 153.224, 179.76, 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) Cl 3 17.00 S 124 16.00 O 4408 8.00 N 3872 7.00 C 15067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.65 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 902 " - " ASN A 368 " " NAG B 901 " - " ASN B 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN C 368 " " NAG G 1 " - " ASN D 688 " Time building additional restraints: 9.72 Conformation dependent library (CDL) restraints added in 4.5 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 32 sheets defined 38.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 removed outlier: 4.210A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.878A pdb=" N SER A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 112 removed outlier: 4.826A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.956A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.556A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.616A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.579A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 256 through 261 removed outlier: 4.068A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 295 removed outlier: 3.703A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 removed outlier: 4.020A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.611A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 560 through 583 removed outlier: 3.989A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.584A pdb=" N SER A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 654 removed outlier: 3.962A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 700 through 706 removed outlier: 3.688A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 removed outlier: 3.694A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.601A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 removed outlier: 3.975A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 792 Processing helix chain 'A' and resid 810 through 840 removed outlier: 4.274A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.993A pdb=" N GLU B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 removed outlier: 3.508A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.667A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 247 Processing helix chain 'B' and resid 290 through 311 removed outlier: 3.568A pdb=" N ARG B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 329 removed outlier: 3.916A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 329' Processing helix chain 'B' and resid 333 through 339 Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 549 through 552 No H-bonds generated for 'chain 'B' and resid 549 through 552' Processing helix chain 'B' and resid 558 through 578 removed outlier: 3.524A pdb=" N MET B 565 " --> pdb=" O MET B 561 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 613 Processing helix chain 'B' and resid 626 through 655 removed outlier: 3.507A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 690 through 698 removed outlier: 3.587A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 771 through 786 removed outlier: 3.700A pdb=" N ARG B 774 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP B 786 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 796 Processing helix chain 'B' and resid 815 through 844 removed outlier: 5.657A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 51 removed outlier: 4.291A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 85 removed outlier: 4.497A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.574A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 129 Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.629A pdb=" N GLN C 147 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER C 148 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR C 158 " --> pdb=" O MET C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 187 removed outlier: 3.851A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 removed outlier: 3.651A pdb=" N MET C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 205 through 213' Processing helix chain 'C' and resid 225 through 235 removed outlier: 3.501A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.534A pdb=" N LEU C 259 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.590A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 325 Processing helix chain 'C' and resid 458 through 470 removed outlier: 3.530A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 506 removed outlier: 3.596A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 525 No H-bonds generated for 'chain 'C' and resid 523 through 525' Processing helix chain 'C' and resid 553 through 556 No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 560 through 583 removed outlier: 3.732A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 615 removed outlier: 3.506A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TRP C 611 " --> pdb=" O MET C 607 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 656 removed outlier: 3.562A pdb=" N ILE C 631 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY C 633 " --> pdb=" O ARG C 630 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 635 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA C 637 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 650 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 656 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 673 No H-bonds generated for 'chain 'C' and resid 670 through 673' Processing helix chain 'C' and resid 688 through 695 Processing helix chain 'C' and resid 697 through 707 removed outlier: 5.417A pdb=" N THR C 701 " --> pdb=" O GLU C 698 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 704 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 707 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 722 removed outlier: 3.534A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 722 " --> pdb=" O ILE C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.629A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 781 removed outlier: 3.831A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 792 removed outlier: 3.519A pdb=" N LEU C 788 " --> pdb=" O PHE C 784 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 789 " --> pdb=" O MET C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 839 removed outlier: 3.821A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 830 " --> pdb=" O ALA C 826 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 107 through 118 removed outlier: 3.583A pdb=" N PHE D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 150 through 158 removed outlier: 3.789A pdb=" N LEU D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 No H-bonds generated for 'chain 'D' and resid 160 through 163' Processing helix chain 'D' and resid 180 through 191 Processing helix chain 'D' and resid 213 through 222 removed outlier: 3.705A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 247 Processing helix chain 'D' and resid 260 through 263 No H-bonds generated for 'chain 'D' and resid 260 through 263' Processing helix chain 'D' and resid 289 through 308 Processing helix chain 'D' and resid 325 through 329 removed outlier: 4.222A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 329' Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.722A pdb=" N ILE D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 502 Processing helix chain 'D' and resid 517 through 520 No H-bonds generated for 'chain 'D' and resid 517 through 520' Processing helix chain 'D' and resid 556 through 578 removed outlier: 3.810A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 613 Processing helix chain 'D' and resid 626 through 656 removed outlier: 3.746A pdb=" N VAL D 634 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP D 635 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA D 644 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE D 653 " --> pdb=" O ASN D 649 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 690 through 696 Processing helix chain 'D' and resid 700 through 709 removed outlier: 4.695A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE D 709 " --> pdb=" O TYR D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 722 removed outlier: 3.738A pdb=" N LYS D 722 " --> pdb=" O LEU D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.526A pdb=" N ASN D 737 " --> pdb=" O ALA D 733 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 742 " --> pdb=" O TYR D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 786 removed outlier: 3.522A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 796 Processing helix chain 'D' and resid 818 through 844 Processing sheet with id= A, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.747A pdb=" N LEU A 165 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 195 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 197 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL A 246 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU A 221 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 248 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 267 through 271 Processing sheet with id= D, first strand: chain 'A' and resid 366 through 368 removed outlier: 4.235A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 373 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 397 through 400 removed outlier: 7.197A pdb=" N THR A 473 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE A 400 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLU A 475 " --> pdb=" O ILE A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.674A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS A 454 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 451 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 487 through 489 Processing sheet with id= H, first strand: chain 'A' and resid 534 through 536 removed outlier: 4.197A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 728 through 732 removed outlier: 3.908A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 67 through 73 removed outlier: 3.559A pdb=" N LEU B 41 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B 73 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ALA B 38 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL B 97 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE B 40 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE B 99 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL B 42 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE B 99 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 124 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.472A pdb=" N THR B 255 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU B 230 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 257 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 278 through 282 removed outlier: 4.090A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP B 379 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 408 through 410 removed outlier: 3.652A pdb=" N THR B 410 " --> pdb=" O TYR B 479 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 418 through 420 removed outlier: 4.322A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 534 through 537 removed outlier: 3.506A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.067A pdb=" N GLN C 59 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE C 29 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN C 61 " --> pdb=" O ILE C 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 30 through 32 Processing sheet with id= R, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.698A pdb=" N PHE C 197 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL C 246 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 248 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 350 through 352 removed outlier: 3.907A pdb=" N TYR C 351 " --> pdb=" O TYR C 367 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE C 366 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 373 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 354 through 357 Processing sheet with id= U, first strand: chain 'C' and resid 397 through 402 removed outlier: 6.820A pdb=" N THR C 473 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE C 400 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU C 475 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N THR C 402 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N HIS C 477 " --> pdb=" O THR C 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.662A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 412 " --> pdb=" O CYS C 454 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS C 454 " --> pdb=" O LYS C 412 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 486 through 489 Processing sheet with id= X, first strand: chain 'C' and resid 527 through 529 Processing sheet with id= Y, first strand: chain 'C' and resid 534 through 537 removed outlier: 4.260A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 729 through 732 removed outlier: 3.951A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.697A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 39 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY D 96 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N PHE D 99 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU D 124 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 202 through 204 removed outlier: 7.205A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR D 255 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU D 230 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE D 257 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 278 through 282 removed outlier: 3.796A pdb=" N LEU D 362 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 378 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 385 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 380 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 408 through 410 Processing sheet with id= AE, first strand: chain 'D' and resid 418 through 420 removed outlier: 4.082A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 729 through 732 803 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.83 Time building geometry restraints manager: 10.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3852 1.28 - 1.42: 6085 1.42 - 1.56: 13807 1.56 - 1.70: 7 1.70 - 1.84: 213 Bond restraints: 23964 Sorted by residual: bond pdb=" CA LYS D 438 " pdb=" C LYS D 438 " ideal model delta sigma weight residual 1.524 1.401 0.123 1.23e-02 6.61e+03 9.97e+01 bond pdb=" CA PHE B 642 " pdb=" C PHE B 642 " ideal model delta sigma weight residual 1.524 1.418 0.106 1.24e-02 6.50e+03 7.32e+01 bond pdb=" C GLN B 437 " pdb=" O GLN B 437 " ideal model delta sigma weight residual 1.236 1.137 0.099 1.19e-02 7.06e+03 6.86e+01 bond pdb=" CA ALA D 636 " pdb=" C ALA D 636 " ideal model delta sigma weight residual 1.523 1.420 0.103 1.30e-02 5.92e+03 6.30e+01 bond pdb=" C TRP D 610 " pdb=" O TRP D 610 " ideal model delta sigma weight residual 1.237 1.146 0.091 1.17e-02 7.31e+03 6.03e+01 ... (remaining 23959 not shown) Histogram of bond angle deviations from ideal: 90.73 - 99.39: 5 99.39 - 108.06: 1066 108.06 - 116.72: 15848 116.72 - 125.39: 15397 125.39 - 134.06: 397 Bond angle restraints: 32713 Sorted by residual: angle pdb=" C ILE D 606 " pdb=" CA ILE D 606 " pdb=" CB ILE D 606 " ideal model delta sigma weight residual 112.14 95.86 16.28 1.35e+00 5.49e-01 1.45e+02 angle pdb=" C VAL D 613 " pdb=" CA VAL D 613 " pdb=" CB VAL D 613 " ideal model delta sigma weight residual 112.14 99.54 12.60 1.35e+00 5.49e-01 8.71e+01 angle pdb=" N LEU C 655 " pdb=" CA LEU C 655 " pdb=" C LEU C 655 " ideal model delta sigma weight residual 111.14 119.84 -8.70 1.08e+00 8.57e-01 6.49e+01 angle pdb=" N GLN D 437 " pdb=" CA GLN D 437 " pdb=" C GLN D 437 " ideal model delta sigma weight residual 108.02 121.49 -13.47 1.75e+00 3.27e-01 5.93e+01 angle pdb=" CA LEU D 612 " pdb=" CB LEU D 612 " pdb=" CG LEU D 612 " ideal model delta sigma weight residual 116.30 90.73 25.57 3.50e+00 8.16e-02 5.34e+01 ... (remaining 32708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 13595 24.60 - 49.19: 604 49.19 - 73.79: 80 73.79 - 98.38: 26 98.38 - 122.98: 5 Dihedral angle restraints: 14310 sinusoidal: 5157 harmonic: 9153 Sorted by residual: dihedral pdb=" CB CYS C 436 " pdb=" SG CYS C 436 " pdb=" SG CYS C 455 " pdb=" CB CYS C 455 " ideal model delta sinusoidal sigma weight residual -86.00 -162.29 76.29 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS D 429 " pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 166.62 -73.62 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 457 " pdb=" CB CYS B 457 " ideal model delta sinusoidal sigma weight residual 93.00 165.48 -72.48 1 1.00e+01 1.00e-02 6.71e+01 ... (remaining 14307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.068: 3915 1.068 - 2.137: 0 2.137 - 3.205: 0 3.205 - 4.274: 0 4.274 - 5.342: 3 Chirality restraints: 3918 Sorted by residual: chirality pdb=" C1 AJC9 B 903 " pdb=" C2 AJC9 B 903 " pdb=" C5 AJC9 B 903 " pdb=" C7 AJC9 B 903 " both_signs ideal model delta sigma weight residual False 2.73 -2.61 5.34 2.00e-01 2.50e+01 7.13e+02 chirality pdb=" C1 CJC9 B 903 " pdb=" C2 CJC9 B 903 " pdb=" C5 CJC9 B 903 " pdb=" C7 CJC9 B 903 " both_signs ideal model delta sigma weight residual False 2.73 -2.59 5.32 2.00e-01 2.50e+01 7.07e+02 chirality pdb=" C1 BJC9 B 903 " pdb=" C2 BJC9 B 903 " pdb=" C5 BJC9 B 903 " pdb=" C7 BJC9 B 903 " both_signs ideal model delta sigma weight residual False 2.73 -2.51 5.24 2.00e-01 2.50e+01 6.87e+02 ... (remaining 3915 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 435 " 0.031 2.00e-02 2.50e+03 6.13e-02 3.76e+01 pdb=" C PRO B 435 " -0.106 2.00e-02 2.50e+03 pdb=" O PRO B 435 " 0.039 2.00e-02 2.50e+03 pdb=" N CYS B 436 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 678 " 0.097 5.00e-02 4.00e+02 1.46e-01 3.42e+01 pdb=" N PRO B 679 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO B 679 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO B 679 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 678 " -0.082 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO D 679 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO D 679 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO D 679 " -0.064 5.00e-02 4.00e+02 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 42 2.41 - 3.03: 14210 3.03 - 3.65: 33258 3.65 - 4.28: 44988 4.28 - 4.90: 75406 Nonbonded interactions: 167904 Sorted by model distance: nonbonded pdb=" CD1 LEU D 609 " pdb=" NE1 TRP D 635 " model vdw 1.784 3.540 nonbonded pdb=" OE2 GLU D 151 " pdb=" NZ LYS D 185 " model vdw 2.202 2.520 nonbonded pdb=" OH TYR D 507 " pdb=" OG SER D 770 " model vdw 2.205 2.440 nonbonded pdb=" OD1 ASP B 101 " pdb=" N ASP B 102 " model vdw 2.210 2.520 nonbonded pdb=" O MET A 125 " pdb=" NH2 ARG A 139 " model vdw 2.217 2.520 ... (remaining 167899 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 41 or (resid 42 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 or (resid 47 through 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 72 or (res \ id 73 through 75 and (name N or name CA or name C or name O or name CB )) or res \ id 76 through 129 or (resid 130 through 131 and (name N or name CA or name C or \ name O or name CB )) or resid 132 through 214 or (resid 215 through 216 and (nam \ e N or name CA or name C or name O or name CB )) or resid 217 through 259 or (re \ sid 260 and (name N or name CA or name C or name O or name CB )) or resid 261 th \ rough 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) \ or resid 276 through 289 or (resid 290 through 291 and (name N or name CA or na \ me C or name O or name CB )) or resid 292 or (resid 293 through 294 and (name N \ or name CA or name C or name O or name CB )) or resid 295 through 325 or (resid \ 326 and (name N or name CA or name C or name O or name CB )) or resid 327 throug \ h 338 or (resid 339 and (name N or name CA or name C or name O or name CB )) or \ resid 340 through 342 or (resid 343 and (name N or name CA or name C or name O o \ r name CB )) or (resid 344 through 346 and (name N or name CA or name C or name \ O or name CB )) or resid 347 through 358 or (resid 359 through 360 and (name N o \ r name CA or name C or name O or name CB )) or resid 361 through 377 or (resid 3 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 379 through \ 575 or (resid 576 and (name N or name CA or name C or name O or name CB )) or r \ esid 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) \ or resid 579 through 580 or (resid 581 through 583 and (name N or name CA or nam \ e C or name O or name CB )) or resid 584 through 606 or (resid 607 and (name N o \ r name CA or name C or name O or name CB )) or resid 608 through 657 or (resid 6 \ 58 through 659 and (name N or name CA or name C or name O or name CB )) or resid \ 660 through 677 or (resid 678 and (name N or name CA or name C or name O or nam \ e CB )) or resid 679 through 707 or (resid 708 and (name N or name CA or name C \ or name O or name CB )) or resid 709 through 798 or (resid 799 and (name N or na \ me CA or name C or name O or name CB )) or resid 800 through 841 or resid 901 th \ rough 903)) selection = (chain 'C' and (resid 25 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 or (resid 61 through 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 through 82 or (resid 83 and ( \ name N or name CA or name C or name O or name CB )) or resid 84 through 101 or ( \ resid 102 and (name N or name CA or name C or name O or name CB )) or resid 103 \ through 114 or (resid 115 and (name N or name CA or name C or name O or name CB \ )) or resid 116 through 130 or (resid 131 and (name N or name CA or name C or na \ me O or name CB )) or resid 132 through 155 or (resid 156 and (name N or name CA \ or name C or name O or name CB )) or resid 157 through 184 or (resid 185 throug \ h 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thro \ ugh 224 or (resid 225 and (name N or name CA or name C or name O or name CB )) o \ r resid 226 through 271 or (resid 272 and (name N or name CA or name C or name O \ or name CB )) or resid 273 through 386 or (resid 387 through 388 and (name N or \ name CA or name C or name O or name CB )) or resid 389 or (resid 390 and (name \ N or name CA or name C or name O or name CB )) or resid 391 through 633 or (resi \ d 634 and (name N or name CA or name C or name O or name CB )) or resid 635 thro \ ugh 676 or (resid 677 through 678 and (name N or name CA or name C or name O or \ name CB )) or resid 679 through 781 or (resid 782 and (name N or name CA or name \ C or name O or name CB )) or resid 783 through 789 or (resid 790 and (name N or \ name CA or name C or name O or name CB )) or resid 791 through 793 or (resid 79 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 795 through \ 841 or resid 901 through 903)) } ncs_group { reference = (chain 'B' and (resid 34 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 or (resid 69 and (name N or name CA or nam \ e C or name O or name CB )) or resid 70 through 83 or (resid 84 and (name N or n \ ame CA or name C or name O or name CB )) or resid 85 through 117 or (resid 118 a \ nd (name N or name CA or name C or name O or name CB )) or resid 119 through 136 \ or (resid 137 and (name N or name CA or name C or name O or name CB )) or resid \ 138 or (resid 139 and (name N or name CA or name C or name O or name CB )) or r \ esid 140 through 212 or (resid 213 and (name N or name CA or name C or name O or \ name CB )) or resid 214 through 305 or (resid 306 through 308 and (name N or na \ me CA or name C or name O or name CB )) or resid 309 or (resid 310 and (name N o \ r name CA or name C or name O or name CB )) or resid 311 through 315 or (resid 3 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 317 through \ 332 or (resid 333 through 334 and (name N or name CA or name C or name O or nam \ e CB )) or resid 335 through 346 or (resid 347 through 348 and (name N or name C \ A or name C or name O or name CB )) or resid 349 through 360 or (resid 361 and ( \ name N or name CA or name C or name O or name CB )) or resid 362 through 440 or \ (resid 441 and (name N or name CA or name C or name O or name CB )) or resid 442 \ through 520 or (resid 521 and (name N or name CA or name C or name O or name CB \ )) or resid 522 through 562 or (resid 563 and (name N or name CA or name C or n \ ame O or name CB )) or resid 564 through 711 or (resid 712 and (name N or name C \ A or name C or name O or name CB )) or resid 713 through 746 or (resid 747 and ( \ name N or name CA or name C or name O or name CB )) or resid 748 through 802 or \ (resid 803 through 807 and (name N or name CA or name C or name O or name CB )) \ or resid 808 through 811 or (resid 812 and (name N or name CA or name C or name \ O or name CB )) or resid 813 through 817 or (resid 818 through 819 and (name N o \ r name CA or name C or name O or name CB )) or resid 820 through 823 or (resid 8 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 825 through \ 828 or (resid 829 through 830 and (name N or name CA or name C or name O or nam \ e CB )) or resid 831 through 835 or (resid 836 and (name N or name CA or name C \ or name O or name CB )) or resid 837 through 845 or resid 901)) selection = (chain 'D' and (resid 34 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 197 or (resid 198 and (name N or n \ ame CA or name C or name O or name CB )) or resid 199 or (resid 200 through 201 \ and (name N or name CA or name C or name O or name CB )) or resid 202 through 20 \ 6 or (resid 207 and (name N or name CA or name C or name O or name CB )) or resi \ d 208 or (resid 209 through 211 and (name N or name CA or name C or name O or na \ me CB )) or resid 212 through 377 or (resid 378 and (name N or name CA or name C \ or name O or name CB )) or resid 379 through 502 or (resid 503 and (name N or n \ ame CA or name C or name O or name CB )) or resid 504 through 560 or (resid 561 \ and (name N or name CA or name C or name O or name CB )) or resid 562 through 57 \ 4 or (resid 575 and (name N or name CA or name C or name O or name CB )) or resi \ d 576 through 628 or (resid 629 and (name N or name CA or name C or name O or na \ me CB )) or resid 630 through 661 or (resid 662 and (name N or name CA or name C \ or name O or name CB )) or resid 663 through 669 or (resid 670 and (name N or n \ ame CA or name C or name O or name CB )) or resid 671 through 672 or (resid 673 \ and (name N or name CA or name C or name O or name CB )) or resid 674 through 67 \ 5 or (resid 676 through 677 and (name N or name CA or name C or name O or name C \ B )) or resid 678 through 805 or (resid 806 through 807 and (name N or name CA o \ r name C or name O or name CB )) or resid 808 through 815 or (resid 816 and (nam \ e N or name CA or name C or name O or name CB )) or resid 817 through 845 or res \ id 901)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.33 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 15.210 Check model and map are aligned: 0.320 Set scattering table: 0.250 Process input model: 63.650 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 0.135 23964 Z= 0.512 Angle : 0.814 25.573 32713 Z= 0.456 Chirality : 0.157 5.342 3918 Planarity : 0.006 0.146 4139 Dihedral : 14.175 122.981 8357 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.01 % Favored : 94.64 % Rotamer: Outliers : 0.90 % Allowed : 0.73 % Favored : 98.37 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.77 (0.15), residues: 3136 helix: 0.95 (0.15), residues: 1121 sheet: -0.18 (0.29), residues: 359 loop : -1.69 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 607 HIS 0.014 0.001 HIS D 311 PHE 0.061 0.001 PHE D 642 TYR 0.064 0.001 TYR D 646 ARG 0.006 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 355 time to evaluate : 2.615 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8180 (tpp) cc_final: 0.7849 (tpp) REVERT: B 307 MET cc_start: 0.6990 (ppp) cc_final: 0.6420 (tmm) REVERT: B 347 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7533 (mtm-85) REVERT: B 432 ASN cc_start: 0.8784 (m-40) cc_final: 0.8576 (p0) REVERT: B 782 GLN cc_start: 0.8309 (tp-100) cc_final: 0.7812 (tp-100) REVERT: C 153 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7719 (mm-30) REVERT: C 209 MET cc_start: 0.7611 (tpp) cc_final: 0.7085 (tpp) REVERT: C 528 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7380 (tm-30) REVERT: C 651 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9192 (tt) REVERT: D 89 MET cc_start: 0.5658 (mmp) cc_final: 0.4711 (ttp) REVERT: D 95 GLN cc_start: 0.7360 (mm-40) cc_final: 0.6851 (tt0) REVERT: D 436 CYS cc_start: 0.5619 (p) cc_final: 0.5404 (p) REVERT: D 561 MET cc_start: 0.8577 (ppp) cc_final: 0.8145 (ppp) REVERT: D 612 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9377 (tt) REVERT: D 645 SER cc_start: 0.9667 (OUTLIER) cc_final: 0.9419 (p) REVERT: D 706 MET cc_start: 0.7247 (tmm) cc_final: 0.7009 (tmm) outliers start: 21 outliers final: 13 residues processed: 375 average time/residue: 0.2948 time to fit residues: 185.9801 Evaluate side-chains 303 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 286 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 654 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 0.0170 chunk 237 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 160 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 285 optimal weight: 8.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 796 GLN B 437 GLN C 146 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 219 GLN D 311 HIS D 656 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 23964 Z= 0.332 Angle : 0.771 29.048 32713 Z= 0.364 Chirality : 0.080 2.418 3918 Planarity : 0.006 0.147 4139 Dihedral : 8.890 98.061 3664 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.57 % Favored : 93.14 % Rotamer: Outliers : 2.10 % Allowed : 9.95 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.00 (0.15), residues: 3136 helix: 0.67 (0.15), residues: 1149 sheet: -0.30 (0.27), residues: 382 loop : -1.82 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 379 HIS 0.007 0.001 HIS A 780 PHE 0.030 0.002 PHE D 114 TYR 0.014 0.001 TYR B 479 ARG 0.005 0.000 ARG D 774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 300 time to evaluate : 2.748 Fit side-chains revert: symmetry clash REVERT: B 101 ASP cc_start: 0.7159 (t0) cc_final: 0.6878 (t0) REVERT: B 309 SER cc_start: 0.7361 (t) cc_final: 0.6992 (m) REVERT: B 432 ASN cc_start: 0.8756 (m-40) cc_final: 0.8425 (p0) REVERT: B 782 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7684 (tp-100) REVERT: C 153 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8067 (mm-30) REVERT: C 354 MET cc_start: 0.7765 (ppp) cc_final: 0.7439 (ppp) REVERT: C 737 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7672 (mt-10) REVERT: D 89 MET cc_start: 0.5840 (mmp) cc_final: 0.5213 (ttp) REVERT: D 95 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7098 (pt0) REVERT: D 386 MET cc_start: 0.8798 (mmm) cc_final: 0.8322 (tpp) REVERT: D 561 MET cc_start: 0.8595 (ppp) cc_final: 0.8146 (ppp) REVERT: D 562 MET cc_start: 0.8830 (ttt) cc_final: 0.8550 (ttt) REVERT: D 706 MET cc_start: 0.7369 (tmm) cc_final: 0.7095 (tmm) outliers start: 49 outliers final: 32 residues processed: 327 average time/residue: 0.2934 time to fit residues: 164.2187 Evaluate side-chains 307 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 274 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 237 optimal weight: 0.0870 chunk 194 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 285 optimal weight: 7.9990 chunk 308 optimal weight: 0.7980 chunk 254 optimal weight: 8.9990 chunk 283 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 229 optimal weight: 0.3980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 23964 Z= 0.171 Angle : 0.703 28.272 32713 Z= 0.319 Chirality : 0.078 2.462 3918 Planarity : 0.005 0.145 4139 Dihedral : 7.821 98.107 3639 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.94 % Favored : 94.80 % Rotamer: Outliers : 1.80 % Allowed : 12.40 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.00 % 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: -0.79 (0.15), residues: 3136 helix: 0.85 (0.15), residues: 1158 sheet: -0.22 (0.28), residues: 379 loop : -1.70 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 379 HIS 0.003 0.001 HIS C 709 PHE 0.025 0.001 PHE D 114 TYR 0.019 0.001 TYR A 578 ARG 0.004 0.000 ARG D 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 302 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9261 (tt) cc_final: 0.8834 (pp) REVERT: B 101 ASP cc_start: 0.7173 (t0) cc_final: 0.6765 (t0) REVERT: B 432 ASN cc_start: 0.8761 (m-40) cc_final: 0.8416 (p0) REVERT: B 565 MET cc_start: 0.8049 (mtm) cc_final: 0.7564 (mtp) REVERT: B 653 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7594 (t80) REVERT: B 727 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7475 (t0) REVERT: C 153 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 184 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8176 (mp) REVERT: C 354 MET cc_start: 0.7668 (ppp) cc_final: 0.7228 (ppp) REVERT: C 355 ASN cc_start: 0.8514 (t0) cc_final: 0.7629 (t0) REVERT: C 737 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7580 (mt-10) REVERT: D 89 MET cc_start: 0.5937 (mmp) cc_final: 0.5056 (ttp) REVERT: D 524 ASP cc_start: 0.8177 (t0) cc_final: 0.7782 (t0) REVERT: D 561 MET cc_start: 0.8598 (ppp) cc_final: 0.8198 (ppp) REVERT: D 645 SER cc_start: 0.9535 (m) cc_final: 0.9126 (p) REVERT: D 706 MET cc_start: 0.7361 (tmm) cc_final: 0.7069 (tmm) outliers start: 42 outliers final: 29 residues processed: 325 average time/residue: 0.2795 time to fit residues: 154.6636 Evaluate side-chains 304 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 272 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 808 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 0.6980 chunk 214 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 31 optimal weight: 0.0770 chunk 136 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 286 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 271 optimal weight: 0.0570 chunk 81 optimal weight: 30.0000 overall best weight: 1.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 23964 Z= 0.193 Angle : 0.695 27.558 32713 Z= 0.315 Chirality : 0.077 2.431 3918 Planarity : 0.005 0.144 4139 Dihedral : 7.375 98.306 3634 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.77 % Favored : 93.97 % Rotamer: Outliers : 2.19 % Allowed : 14.63 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.00 % 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: -0.74 (0.15), residues: 3136 helix: 0.93 (0.16), residues: 1162 sheet: -0.27 (0.27), residues: 397 loop : -1.69 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.003 0.001 HIS C 709 PHE 0.024 0.001 PHE D 114 TYR 0.016 0.001 TYR D 479 ARG 0.003 0.000 ARG D 774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 294 time to evaluate : 2.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 TYR cc_start: 0.7189 (m-80) cc_final: 0.6784 (m-10) REVERT: A 341 ASN cc_start: 0.6921 (p0) cc_final: 0.6414 (p0) REVERT: A 565 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8896 (pp) REVERT: B 101 ASP cc_start: 0.7320 (t0) cc_final: 0.6938 (t0) REVERT: B 432 ASN cc_start: 0.8766 (m-40) cc_final: 0.8395 (p0) REVERT: B 727 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7487 (t0) REVERT: C 153 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8114 (mm-30) REVERT: C 184 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8142 (mp) REVERT: C 354 MET cc_start: 0.7893 (ppp) cc_final: 0.7471 (ppp) REVERT: C 355 ASN cc_start: 0.8649 (t0) cc_final: 0.7773 (t0) REVERT: C 674 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8415 (p0) REVERT: C 737 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7598 (mt-10) REVERT: D 89 MET cc_start: 0.5830 (mmp) cc_final: 0.4850 (ttp) REVERT: D 386 MET cc_start: 0.8575 (mmm) cc_final: 0.8129 (tpp) REVERT: D 561 MET cc_start: 0.8615 (ppp) cc_final: 0.8218 (ppp) REVERT: D 706 MET cc_start: 0.7412 (tmm) cc_final: 0.7126 (tmm) outliers start: 51 outliers final: 31 residues processed: 319 average time/residue: 0.2753 time to fit residues: 150.7785 Evaluate side-chains 308 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 273 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 0.0270 chunk 272 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 HIS C 146 HIS C 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 23964 Z= 0.252 Angle : 0.714 24.707 32713 Z= 0.326 Chirality : 0.077 2.440 3918 Planarity : 0.005 0.143 4139 Dihedral : 7.185 99.282 3632 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.51 % Favored : 93.24 % Rotamer: Outliers : 2.70 % Allowed : 16.00 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.77 (0.15), residues: 3136 helix: 0.96 (0.16), residues: 1165 sheet: -0.40 (0.27), residues: 403 loop : -1.73 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 379 HIS 0.003 0.001 HIS C 709 PHE 0.024 0.001 PHE D 114 TYR 0.021 0.001 TYR A 578 ARG 0.002 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 281 time to evaluate : 2.801 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7818 (pp20) REVERT: A 341 ASN cc_start: 0.6933 (p0) cc_final: 0.6396 (p0) REVERT: A 565 LEU cc_start: 0.9253 (tt) cc_final: 0.8868 (pp) REVERT: B 101 ASP cc_start: 0.7450 (t0) cc_final: 0.7140 (t0) REVERT: B 432 ASN cc_start: 0.8742 (m-40) cc_final: 0.8386 (p0) REVERT: B 563 PHE cc_start: 0.8258 (t80) cc_final: 0.7812 (t80) REVERT: B 653 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7738 (t80) REVERT: B 727 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7627 (t0) REVERT: B 782 GLN cc_start: 0.7922 (tp40) cc_final: 0.7641 (tp40) REVERT: B 791 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7933 (tm-30) REVERT: C 153 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8116 (mm-30) REVERT: C 184 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8174 (mp) REVERT: C 354 MET cc_start: 0.8011 (ppp) cc_final: 0.7619 (ppp) REVERT: C 355 ASN cc_start: 0.8764 (t0) cc_final: 0.7943 (t0) REVERT: C 460 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8341 (mp) REVERT: C 470 MET cc_start: 0.8962 (mpp) cc_final: 0.8708 (mpp) REVERT: C 674 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8473 (p0) REVERT: C 737 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7596 (mt-10) REVERT: D 386 MET cc_start: 0.8612 (mmm) cc_final: 0.8198 (tpp) REVERT: D 561 MET cc_start: 0.8589 (ppp) cc_final: 0.8262 (ppp) REVERT: D 565 MET cc_start: 0.8433 (tpp) cc_final: 0.8194 (tpp) REVERT: D 654 MET cc_start: 0.8554 (mmp) cc_final: 0.8166 (mmt) REVERT: D 706 MET cc_start: 0.7473 (tmm) cc_final: 0.7163 (tmm) outliers start: 63 outliers final: 35 residues processed: 315 average time/residue: 0.2723 time to fit residues: 148.1135 Evaluate side-chains 312 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 271 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 4.9990 chunk 273 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 303 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 159 optimal weight: 0.0070 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.106 23964 Z= 0.159 Angle : 0.682 25.003 32713 Z= 0.306 Chirality : 0.076 2.422 3918 Planarity : 0.005 0.140 4139 Dihedral : 6.624 97.097 3631 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.20 % Favored : 94.55 % Rotamer: Outliers : 2.10 % Allowed : 17.42 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.64 (0.15), residues: 3136 helix: 1.07 (0.16), residues: 1174 sheet: -0.36 (0.27), residues: 411 loop : -1.67 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 563 HIS 0.002 0.000 HIS A 146 PHE 0.016 0.001 PHE D 114 TYR 0.018 0.001 TYR A 578 ARG 0.003 0.000 ARG D 774 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 290 time to evaluate : 2.669 Fit side-chains revert: symmetry clash REVERT: A 261 TYR cc_start: 0.7124 (m-80) cc_final: 0.6683 (m-10) REVERT: A 341 ASN cc_start: 0.6902 (p0) cc_final: 0.6376 (p0) REVERT: A 437 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8818 (p) REVERT: A 565 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8849 (pp) REVERT: B 101 ASP cc_start: 0.7465 (t0) cc_final: 0.7077 (t0) REVERT: B 134 MET cc_start: 0.6341 (tmm) cc_final: 0.5975 (tmm) REVERT: B 432 ASN cc_start: 0.8757 (m-40) cc_final: 0.8379 (p0) REVERT: B 563 PHE cc_start: 0.8332 (t80) cc_final: 0.7830 (t80) REVERT: B 653 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7727 (t80) REVERT: B 727 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7632 (t0) REVERT: B 791 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 153 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8134 (mm-30) REVERT: C 354 MET cc_start: 0.7967 (ppp) cc_final: 0.7606 (ppp) REVERT: C 460 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8332 (mp) REVERT: C 470 MET cc_start: 0.8912 (mpp) cc_final: 0.8576 (mpp) REVERT: C 737 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7547 (mt-10) REVERT: C 817 PHE cc_start: 0.8393 (m-80) cc_final: 0.8156 (m-80) REVERT: D 386 MET cc_start: 0.8606 (mmm) cc_final: 0.8253 (tpp) REVERT: D 561 MET cc_start: 0.8561 (ppp) cc_final: 0.8208 (ppp) REVERT: D 565 MET cc_start: 0.8437 (tpp) cc_final: 0.8194 (tpp) REVERT: D 654 MET cc_start: 0.8456 (mmp) cc_final: 0.8068 (mmt) REVERT: D 706 MET cc_start: 0.7448 (tmm) cc_final: 0.7122 (tmm) REVERT: D 746 CYS cc_start: 0.4349 (OUTLIER) cc_final: 0.3947 (m) outliers start: 49 outliers final: 32 residues processed: 320 average time/residue: 0.2770 time to fit residues: 152.7279 Evaluate side-chains 310 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 272 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 chunk 302 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 184 optimal weight: 0.0030 chunk 139 optimal weight: 10.0000 overall best weight: 3.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS C 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 23964 Z= 0.392 Angle : 0.762 24.899 32713 Z= 0.358 Chirality : 0.079 2.444 3918 Planarity : 0.005 0.140 4139 Dihedral : 6.965 101.029 3631 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.37 % Favored : 92.38 % Rotamer: Outliers : 3.35 % Allowed : 17.55 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.91 (0.15), residues: 3136 helix: 0.87 (0.15), residues: 1169 sheet: -0.60 (0.26), residues: 403 loop : -1.81 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 151 HIS 0.005 0.001 HIS A 371 PHE 0.024 0.002 PHE D 642 TYR 0.020 0.001 TYR A 578 ARG 0.004 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 281 time to evaluate : 2.676 Fit side-chains REVERT: A 341 ASN cc_start: 0.6926 (p0) cc_final: 0.6423 (p0) REVERT: B 101 ASP cc_start: 0.7721 (t0) cc_final: 0.7269 (t0) REVERT: B 563 PHE cc_start: 0.8400 (t80) cc_final: 0.7923 (t80) REVERT: B 653 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 727 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7697 (t0) REVERT: B 782 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7818 (tp-100) REVERT: C 153 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8204 (mm-30) REVERT: C 354 MET cc_start: 0.8128 (ppp) cc_final: 0.7775 (ppp) REVERT: C 460 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 470 MET cc_start: 0.9002 (mpp) cc_final: 0.8687 (mpp) REVERT: C 737 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7624 (mt-10) REVERT: C 752 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8698 (mt) REVERT: C 780 HIS cc_start: 0.9184 (OUTLIER) cc_final: 0.8917 (m-70) REVERT: C 817 PHE cc_start: 0.8373 (m-80) cc_final: 0.8145 (m-80) REVERT: D 386 MET cc_start: 0.8636 (mmm) cc_final: 0.8325 (tpp) REVERT: D 561 MET cc_start: 0.8569 (ppp) cc_final: 0.8320 (ppp) REVERT: D 565 MET cc_start: 0.8550 (tpp) cc_final: 0.8310 (tpp) REVERT: D 654 MET cc_start: 0.8656 (mmp) cc_final: 0.8382 (mmt) REVERT: D 706 MET cc_start: 0.7522 (tmm) cc_final: 0.7154 (tmm) REVERT: D 746 CYS cc_start: 0.4557 (OUTLIER) cc_final: 0.4184 (m) outliers start: 78 outliers final: 53 residues processed: 334 average time/residue: 0.2747 time to fit residues: 159.3644 Evaluate side-chains 332 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 273 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 180 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 237 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS C 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 23964 Z= 0.187 Angle : 0.718 25.249 32713 Z= 0.327 Chirality : 0.077 2.417 3918 Planarity : 0.005 0.138 4139 Dihedral : 7.105 97.291 3631 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.26 % Favored : 94.45 % Rotamer: Outliers : 2.10 % Allowed : 19.48 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.73 (0.15), residues: 3136 helix: 1.03 (0.16), residues: 1164 sheet: -0.55 (0.27), residues: 410 loop : -1.69 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 636 HIS 0.003 0.001 HIS C 371 PHE 0.017 0.001 PHE D 114 TYR 0.024 0.001 TYR C 367 ARG 0.003 0.000 ARG D 774 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 286 time to evaluate : 2.817 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8307 (tpp) cc_final: 0.8067 (tpp) REVERT: A 261 TYR cc_start: 0.7141 (m-80) cc_final: 0.6715 (m-80) REVERT: A 341 ASN cc_start: 0.6865 (p0) cc_final: 0.6351 (p0) REVERT: A 354 MET cc_start: 0.7963 (tpp) cc_final: 0.7610 (tpp) REVERT: A 437 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8861 (p) REVERT: B 101 ASP cc_start: 0.7695 (t0) cc_final: 0.7495 (t0) REVERT: B 432 ASN cc_start: 0.8766 (m-40) cc_final: 0.8459 (p0) REVERT: B 563 PHE cc_start: 0.8376 (t80) cc_final: 0.7904 (t80) REVERT: B 653 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7754 (t80) REVERT: B 727 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7676 (t0) REVERT: B 782 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7621 (tp-100) REVERT: C 153 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7985 (mm-30) REVERT: C 354 MET cc_start: 0.8027 (ppp) cc_final: 0.7717 (ppp) REVERT: C 460 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8427 (mp) REVERT: C 634 MET cc_start: 0.6735 (mmm) cc_final: 0.5747 (mmm) REVERT: C 737 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7549 (mt-10) REVERT: D 151 GLU cc_start: 0.7980 (pt0) cc_final: 0.7366 (pp20) REVERT: D 386 MET cc_start: 0.8605 (mmm) cc_final: 0.8272 (tpp) REVERT: D 561 MET cc_start: 0.8527 (ppp) cc_final: 0.8248 (ppp) REVERT: D 565 MET cc_start: 0.8528 (tpp) cc_final: 0.8296 (tpp) REVERT: D 654 MET cc_start: 0.8507 (mmp) cc_final: 0.8224 (mmt) REVERT: D 706 MET cc_start: 0.7532 (tmm) cc_final: 0.7111 (tmm) REVERT: D 746 CYS cc_start: 0.4182 (OUTLIER) cc_final: 0.3765 (m) outliers start: 49 outliers final: 34 residues processed: 320 average time/residue: 0.2894 time to fit residues: 158.8836 Evaluate side-chains 312 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 273 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 674 ASN Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 2.9990 chunk 289 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 282 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 266 optimal weight: 0.7980 chunk 281 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 817 ASN C 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 23964 Z= 0.210 Angle : 0.719 24.936 32713 Z= 0.327 Chirality : 0.077 2.429 3918 Planarity : 0.005 0.137 4139 Dihedral : 7.502 120.872 3631 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.25 % Favored : 93.46 % Rotamer: Outliers : 2.32 % Allowed : 19.31 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.71 (0.15), residues: 3136 helix: 1.08 (0.16), residues: 1164 sheet: -0.55 (0.27), residues: 398 loop : -1.70 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.003 0.001 HIS A 162 PHE 0.019 0.001 PHE A 42 TYR 0.017 0.001 TYR A 578 ARG 0.003 0.000 ARG C 671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 275 time to evaluate : 2.501 Fit side-chains REVERT: A 261 TYR cc_start: 0.7085 (m-80) cc_final: 0.6656 (m-80) REVERT: A 341 ASN cc_start: 0.6830 (p0) cc_final: 0.6340 (p0) REVERT: A 354 MET cc_start: 0.7905 (tpp) cc_final: 0.7637 (tpp) REVERT: A 565 LEU cc_start: 0.9186 (tt) cc_final: 0.8782 (pp) REVERT: A 707 GLU cc_start: 0.8280 (pp20) cc_final: 0.7987 (tp30) REVERT: B 101 ASP cc_start: 0.7700 (t0) cc_final: 0.7492 (t0) REVERT: B 432 ASN cc_start: 0.8763 (m-40) cc_final: 0.8391 (p0) REVERT: B 563 PHE cc_start: 0.8359 (t80) cc_final: 0.7904 (t80) REVERT: B 653 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7828 (t80) REVERT: B 654 MET cc_start: 0.8338 (ttt) cc_final: 0.8117 (ttm) REVERT: B 727 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7686 (t0) REVERT: B 782 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7735 (tp-100) REVERT: C 153 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8179 (mm-30) REVERT: C 354 MET cc_start: 0.7969 (ppp) cc_final: 0.7662 (ppp) REVERT: C 355 ASN cc_start: 0.8891 (t0) cc_final: 0.8367 (t0) REVERT: C 460 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8463 (mp) REVERT: C 634 MET cc_start: 0.6879 (mmm) cc_final: 0.5883 (mmm) REVERT: C 737 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7567 (mt-10) REVERT: C 817 PHE cc_start: 0.8412 (m-80) cc_final: 0.8155 (m-80) REVERT: D 151 GLU cc_start: 0.7955 (pt0) cc_final: 0.7339 (pp20) REVERT: D 386 MET cc_start: 0.8605 (mmm) cc_final: 0.8287 (tpp) REVERT: D 561 MET cc_start: 0.8528 (ppp) cc_final: 0.8273 (ppp) REVERT: D 565 MET cc_start: 0.8589 (tpp) cc_final: 0.8339 (tpp) REVERT: D 706 MET cc_start: 0.7514 (tmm) cc_final: 0.7151 (tmm) REVERT: D 746 CYS cc_start: 0.4401 (OUTLIER) cc_final: 0.3982 (m) outliers start: 54 outliers final: 44 residues processed: 310 average time/residue: 0.2746 time to fit residues: 145.8948 Evaluate side-chains 323 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 275 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 769 ASP Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 0.0970 chunk 298 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 312 optimal weight: 10.0000 chunk 287 optimal weight: 0.6980 chunk 249 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN C 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 23964 Z= 0.170 Angle : 0.701 25.514 32713 Z= 0.316 Chirality : 0.076 2.421 3918 Planarity : 0.005 0.134 4139 Dihedral : 7.369 120.541 3631 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.64 % Favored : 94.10 % Rotamer: Outliers : 2.19 % Allowed : 19.56 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.61 (0.15), residues: 3136 helix: 1.16 (0.16), residues: 1164 sheet: -0.47 (0.27), residues: 410 loop : -1.65 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.003 0.000 HIS D 359 PHE 0.014 0.001 PHE D 642 TYR 0.016 0.001 TYR A 578 ARG 0.004 0.000 ARG C 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 286 time to evaluate : 2.690 Fit side-chains REVERT: A 74 MET cc_start: 0.8352 (tpp) cc_final: 0.8108 (tpp) REVERT: A 261 TYR cc_start: 0.7109 (m-80) cc_final: 0.6698 (m-80) REVERT: A 341 ASN cc_start: 0.6910 (p0) cc_final: 0.6406 (p0) REVERT: A 354 MET cc_start: 0.7858 (tpp) cc_final: 0.7655 (tpp) REVERT: A 437 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8847 (p) REVERT: A 565 LEU cc_start: 0.9179 (tt) cc_final: 0.8796 (pp) REVERT: B 101 ASP cc_start: 0.7609 (t0) cc_final: 0.7401 (t0) REVERT: B 432 ASN cc_start: 0.8755 (m-40) cc_final: 0.8408 (p0) REVERT: B 563 PHE cc_start: 0.8296 (t80) cc_final: 0.7890 (t80) REVERT: B 653 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7829 (t80) REVERT: B 727 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7672 (t0) REVERT: C 153 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8052 (mm-30) REVERT: C 354 MET cc_start: 0.7913 (ppp) cc_final: 0.7639 (ppp) REVERT: C 355 ASN cc_start: 0.8863 (t0) cc_final: 0.7897 (t0) REVERT: C 634 MET cc_start: 0.6786 (mmm) cc_final: 0.5786 (mmm) REVERT: C 737 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7526 (mt-10) REVERT: C 817 PHE cc_start: 0.8415 (m-80) cc_final: 0.8145 (m-80) REVERT: D 151 GLU cc_start: 0.7923 (pt0) cc_final: 0.7316 (pp20) REVERT: D 386 MET cc_start: 0.8590 (mmm) cc_final: 0.8269 (tpp) REVERT: D 561 MET cc_start: 0.8543 (ppp) cc_final: 0.8236 (ppp) REVERT: D 562 MET cc_start: 0.8832 (ttt) cc_final: 0.8571 (tpp) REVERT: D 565 MET cc_start: 0.8571 (tpp) cc_final: 0.8349 (tpp) REVERT: D 706 MET cc_start: 0.7527 (tmm) cc_final: 0.7214 (tmm) REVERT: D 746 CYS cc_start: 0.4235 (OUTLIER) cc_final: 0.3790 (m) REVERT: D 788 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8681 (mp0) outliers start: 51 outliers final: 40 residues processed: 323 average time/residue: 0.3174 time to fit residues: 176.2227 Evaluate side-chains 320 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 275 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 766 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 SER Chi-restraints excluded: chain D residue 676 ASP Chi-restraints excluded: chain D residue 681 PHE Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 786 ASP Chi-restraints excluded: chain D residue 788 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.4980 chunk 265 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 229 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 249 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 0.0570 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.125791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099483 restraints weight = 54705.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099723 restraints weight = 31144.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.100210 restraints weight = 27654.601| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.102 23964 Z= 0.162 Angle : 0.700 25.731 32713 Z= 0.313 Chirality : 0.076 2.421 3918 Planarity : 0.005 0.132 4139 Dihedral : 7.246 120.440 3631 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.58 % Favored : 94.16 % Rotamer: Outliers : 2.02 % Allowed : 19.69 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.52 (0.15), residues: 3136 helix: 1.22 (0.16), residues: 1171 sheet: -0.39 (0.28), residues: 395 loop : -1.60 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 381 HIS 0.003 0.000 HIS D 405 PHE 0.019 0.001 PHE A 42 TYR 0.017 0.001 TYR A 578 ARG 0.003 0.000 ARG C 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4575.46 seconds wall clock time: 83 minutes 51.49 seconds (5031.49 seconds total)