Starting phenix.real_space_refine on Sun Apr 14 06:32:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbp_23740/04_2024/7mbp_23740.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbp_23740/04_2024/7mbp_23740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbp_23740/04_2024/7mbp_23740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbp_23740/04_2024/7mbp_23740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbp_23740/04_2024/7mbp_23740.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mbp_23740/04_2024/7mbp_23740.pdb" } resolution = 2.8 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 20168 2.51 5 N 5188 2.21 5 O 5176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B GLU 768": "OE1" <-> "OE2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C GLU 768": "OE1" <-> "OE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D GLU 768": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30708 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7574 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 30, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 333 Chain: "B" Number of atoms: 7574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7574 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 30, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 333 Chain: "C" Number of atoms: 7574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7574 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 30, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 333 Chain: "D" Number of atoms: 7574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7574 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 952} Chain breaks: 4 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 30, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 333 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'NAG': 1, 'YUV': 1, 'YUY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 15.81, per 1000 atoms: 0.51 Number of scatterers: 30708 At special positions: 0 Unit cell: (144.838, 144.838, 156.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 5176 8.00 N 5188 7.00 C 20168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 NAG-ASN " NAG A1501 " - " ASN A 921 " " NAG B1501 " - " ASN B 921 " " NAG C1501 " - " ASN C 921 " " NAG D3002 " - " ASN D 921 " Time building additional restraints: 12.20 Conformation dependent library (CDL) restraints added in 5.9 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 8 sheets defined 70.4% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.876A pdb=" N ILE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 89 Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.652A pdb=" N ASN A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.795A pdb=" N LEU A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.543A pdb=" N ILE A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 280 through 298 removed outlier: 3.773A pdb=" N HIS A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 328 Processing helix chain 'A' and resid 334 through 344 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 362 through 376 removed outlier: 4.762A pdb=" N GLU A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 387 Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 412 through 429 removed outlier: 3.534A pdb=" N THR A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.618A pdb=" N VAL A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.758A pdb=" N GLN A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 526 through 545 removed outlier: 3.533A pdb=" N ALA A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS A 543 " --> pdb=" O LYS A 539 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 558 through 574 Processing helix chain 'A' and resid 576 through 584 removed outlier: 3.848A pdb=" N SER A 580 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 602 Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 699 through 714 Processing helix chain 'A' and resid 715 through 740 Processing helix chain 'A' and resid 751 through 774 Processing helix chain 'A' and resid 780 through 791 removed outlier: 3.967A pdb=" N ASP A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 813 removed outlier: 3.594A pdb=" N ALA A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 840 removed outlier: 3.545A pdb=" N MET A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 836 " --> pdb=" O THR A 832 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 882 removed outlier: 4.838A pdb=" N LYS A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 902 removed outlier: 5.057A pdb=" N ARG A 898 " --> pdb=" O ARG A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 925 through 932 Processing helix chain 'A' and resid 942 through 998 removed outlier: 3.712A pdb=" N VAL A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU A 962 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASN A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 990 " --> pdb=" O PHE A 986 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 997 " --> pdb=" O VAL A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 4.121A pdb=" N SER A1009 " --> pdb=" O PHE A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1062 Processing helix chain 'A' and resid 1063 through 1092 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.876A pdb=" N ILE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 89 Processing helix chain 'B' and resid 102 through 119 removed outlier: 3.651A pdb=" N ASN B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.797A pdb=" N LEU B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.543A pdb=" N ILE B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 280 through 298 removed outlier: 3.772A pdb=" N HIS B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 328 Processing helix chain 'B' and resid 334 through 344 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 362 through 376 removed outlier: 4.762A pdb=" N GLU B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 387 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 397 through 407 Processing helix chain 'B' and resid 412 through 429 removed outlier: 3.536A pdb=" N THR B 416 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.619A pdb=" N VAL B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 511 removed outlier: 3.758A pdb=" N GLN B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 524 Processing helix chain 'B' and resid 526 through 545 removed outlier: 3.533A pdb=" N ALA B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS B 543 " --> pdb=" O LYS B 539 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 558 through 574 Processing helix chain 'B' and resid 576 through 584 removed outlier: 3.847A pdb=" N SER B 580 " --> pdb=" O ASP B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 602 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 609 through 622 Processing helix chain 'B' and resid 629 through 639 Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 699 through 714 Processing helix chain 'B' and resid 715 through 740 Processing helix chain 'B' and resid 751 through 774 Processing helix chain 'B' and resid 780 through 791 removed outlier: 3.968A pdb=" N ASP B 791 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 813 removed outlier: 3.594A pdb=" N ALA B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 840 removed outlier: 3.545A pdb=" N MET B 829 " --> pdb=" O ALA B 825 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE B 836 " --> pdb=" O THR B 832 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 882 removed outlier: 4.839A pdb=" N LYS B 857 " --> pdb=" O GLU B 853 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP B 858 " --> pdb=" O ARG B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 902 removed outlier: 5.059A pdb=" N ARG B 898 " --> pdb=" O ARG B 894 " (cutoff:3.500A) Proline residue: B 899 - end of helix Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' Processing helix chain 'B' and resid 908 through 912 Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 925 through 932 Processing helix chain 'B' and resid 942 through 998 removed outlier: 3.713A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU B 962 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 982 " --> pdb=" O GLU B 978 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN B 990 " --> pdb=" O PHE B 986 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1020 removed outlier: 4.118A pdb=" N SER B1009 " --> pdb=" O PHE B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1062 Processing helix chain 'B' and resid 1063 through 1092 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.876A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 89 Processing helix chain 'C' and resid 102 through 119 removed outlier: 3.651A pdb=" N ASN C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.795A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 248 through 260 removed outlier: 3.544A pdb=" N ILE C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 275 Processing helix chain 'C' and resid 280 through 298 removed outlier: 3.773A pdb=" N HIS C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 328 Processing helix chain 'C' and resid 334 through 344 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 362 through 376 removed outlier: 4.761A pdb=" N GLU C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 387 Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 397 through 407 Processing helix chain 'C' and resid 412 through 429 removed outlier: 3.536A pdb=" N THR C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.619A pdb=" N VAL C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.757A pdb=" N GLN C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 524 Processing helix chain 'C' and resid 526 through 545 removed outlier: 3.533A pdb=" N ALA C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS C 543 " --> pdb=" O LYS C 539 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU C 544 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 558 through 574 Processing helix chain 'C' and resid 576 through 584 removed outlier: 3.848A pdb=" N SER C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 602 Processing helix chain 'C' and resid 603 through 608 Processing helix chain 'C' and resid 609 through 622 Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 640 through 645 Processing helix chain 'C' and resid 699 through 714 Processing helix chain 'C' and resid 715 through 740 Processing helix chain 'C' and resid 751 through 774 Processing helix chain 'C' and resid 780 through 791 removed outlier: 3.968A pdb=" N ASP C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 813 removed outlier: 3.594A pdb=" N ALA C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 840 removed outlier: 3.545A pdb=" N MET C 829 " --> pdb=" O ALA C 825 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE C 836 " --> pdb=" O THR C 832 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 882 removed outlier: 4.838A pdb=" N LYS C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP C 858 " --> pdb=" O ARG C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 902 removed outlier: 5.058A pdb=" N ARG C 898 " --> pdb=" O ARG C 894 " (cutoff:3.500A) Proline residue: C 899 - end of helix Processing helix chain 'C' and resid 903 through 905 No H-bonds generated for 'chain 'C' and resid 903 through 905' Processing helix chain 'C' and resid 908 through 912 Processing helix chain 'C' and resid 913 through 917 Processing helix chain 'C' and resid 925 through 932 Processing helix chain 'C' and resid 942 through 998 removed outlier: 3.713A pdb=" N VAL C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 961 " --> pdb=" O THR C 957 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU C 962 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 982 " --> pdb=" O GLU C 978 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 990 " --> pdb=" O PHE C 986 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C 997 " --> pdb=" O VAL C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1020 removed outlier: 4.119A pdb=" N SER C1009 " --> pdb=" O PHE C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1062 Processing helix chain 'C' and resid 1063 through 1092 Processing helix chain 'D' and resid 40 through 51 removed outlier: 3.876A pdb=" N ILE D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 89 Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.651A pdb=" N ASN D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.796A pdb=" N LEU D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 199 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 248 through 260 removed outlier: 3.544A pdb=" N ILE D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 275 Processing helix chain 'D' and resid 280 through 298 removed outlier: 3.775A pdb=" N HIS D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 298 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 328 Processing helix chain 'D' and resid 334 through 344 Processing helix chain 'D' and resid 346 through 354 Processing helix chain 'D' and resid 362 through 376 removed outlier: 4.761A pdb=" N GLU D 368 " --> pdb=" O GLN D 364 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 397 through 407 Processing helix chain 'D' and resid 412 through 429 removed outlier: 3.535A pdb=" N THR D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.617A pdb=" N VAL D 454 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 511 removed outlier: 3.758A pdb=" N GLN D 511 " --> pdb=" O TRP D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 524 Processing helix chain 'D' and resid 526 through 545 removed outlier: 3.533A pdb=" N ALA D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS D 543 " --> pdb=" O LYS D 539 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU D 544 " --> pdb=" O GLU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 556 Processing helix chain 'D' and resid 558 through 574 Processing helix chain 'D' and resid 576 through 584 removed outlier: 3.848A pdb=" N SER D 580 " --> pdb=" O ASP D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 602 Processing helix chain 'D' and resid 603 through 608 Processing helix chain 'D' and resid 609 through 622 Processing helix chain 'D' and resid 629 through 639 Processing helix chain 'D' and resid 640 through 645 Processing helix chain 'D' and resid 699 through 714 Processing helix chain 'D' and resid 715 through 740 Processing helix chain 'D' and resid 751 through 774 Processing helix chain 'D' and resid 780 through 791 removed outlier: 3.968A pdb=" N ASP D 791 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 813 removed outlier: 3.595A pdb=" N ALA D 813 " --> pdb=" O SER D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 840 removed outlier: 3.545A pdb=" N MET D 829 " --> pdb=" O ALA D 825 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE D 836 " --> pdb=" O THR D 832 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 882 removed outlier: 4.837A pdb=" N LYS D 857 " --> pdb=" O GLU D 853 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP D 858 " --> pdb=" O ARG D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 removed outlier: 5.058A pdb=" N ARG D 898 " --> pdb=" O ARG D 894 " (cutoff:3.500A) Proline residue: D 899 - end of helix Processing helix chain 'D' and resid 903 through 905 No H-bonds generated for 'chain 'D' and resid 903 through 905' Processing helix chain 'D' and resid 908 through 912 Processing helix chain 'D' and resid 913 through 917 Processing helix chain 'D' and resid 925 through 932 Processing helix chain 'D' and resid 942 through 998 removed outlier: 3.712A pdb=" N VAL D 946 " --> pdb=" O ALA D 942 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 961 " --> pdb=" O THR D 957 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU D 962 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLU D 978 " --> pdb=" O GLN D 974 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ASN D 979 " --> pdb=" O VAL D 975 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 982 " --> pdb=" O GLU D 978 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN D 990 " --> pdb=" O PHE D 986 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER D 997 " --> pdb=" O VAL D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1020 removed outlier: 4.119A pdb=" N SER D1009 " --> pdb=" O PHE D1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1062 Processing helix chain 'D' and resid 1063 through 1092 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 155 removed outlier: 3.628A pdb=" N TYR A 154 " --> pdb=" O ASP A 21 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A 128 " --> pdb=" O HIS A 173 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE A 175 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY A 130 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 177 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 132 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL A 60 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU A 218 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA A 62 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 243 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP A 240 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS A 304 " --> pdb=" O TRP A 240 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE A 242 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 585 through 586 removed outlier: 3.811A pdb=" N ALA A 592 " --> pdb=" O THR A 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 152 through 155 removed outlier: 3.629A pdb=" N TYR B 154 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 128 " --> pdb=" O HIS B 173 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE B 175 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY B 130 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 177 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 132 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL B 60 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU B 218 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 62 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 243 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TRP B 240 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS B 304 " --> pdb=" O TRP B 240 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE B 242 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 585 through 586 removed outlier: 3.811A pdb=" N ALA B 592 " --> pdb=" O THR B 586 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 152 through 155 removed outlier: 3.627A pdb=" N TYR C 154 " --> pdb=" O ASP C 21 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA C 128 " --> pdb=" O HIS C 173 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE C 175 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY C 130 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 177 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA C 132 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL C 60 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU C 218 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA C 62 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 243 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP C 240 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS C 304 " --> pdb=" O TRP C 240 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE C 242 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 585 through 586 removed outlier: 3.811A pdb=" N ALA C 592 " --> pdb=" O THR C 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 152 through 155 removed outlier: 3.628A pdb=" N TYR D 154 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA D 128 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE D 175 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY D 130 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL D 177 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA D 132 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL D 60 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU D 218 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA D 62 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 243 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP D 240 " --> pdb=" O THR D 302 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS D 304 " --> pdb=" O TRP D 240 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE D 242 " --> pdb=" O HIS D 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 585 through 586 removed outlier: 3.810A pdb=" N ALA D 592 " --> pdb=" O THR D 586 " (cutoff:3.500A) 2034 hydrogen bonds defined for protein. 5982 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: 11.72 Time building geometry restraints manager: 13.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9470 1.34 - 1.46: 4483 1.46 - 1.57: 17267 1.57 - 1.69: 0 1.69 - 1.81: 292 Bond restraints: 31512 Sorted by residual: bond pdb=" C PRO D1003 " pdb=" O PRO D1003 " ideal model delta sigma weight residual 1.243 1.226 0.017 8.50e-03 1.38e+04 4.01e+00 bond pdb=" C PRO C1003 " pdb=" O PRO C1003 " ideal model delta sigma weight residual 1.243 1.226 0.017 8.50e-03 1.38e+04 3.99e+00 bond pdb=" C PRO A1003 " pdb=" O PRO A1003 " ideal model delta sigma weight residual 1.243 1.226 0.017 8.50e-03 1.38e+04 3.99e+00 bond pdb=" C PRO B1003 " pdb=" O PRO B1003 " ideal model delta sigma weight residual 1.243 1.227 0.016 8.50e-03 1.38e+04 3.57e+00 bond pdb=" C3 NAG D3002 " pdb=" O3 NAG D3002 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 31507 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.40: 1004 106.40 - 113.31: 17835 113.31 - 120.23: 10609 120.23 - 127.14: 13211 127.14 - 134.05: 409 Bond angle restraints: 43068 Sorted by residual: angle pdb=" C MET A 917 " pdb=" N PRO A 918 " pdb=" CA PRO A 918 " ideal model delta sigma weight residual 119.85 125.71 -5.86 1.01e+00 9.80e-01 3.36e+01 angle pdb=" C MET D 917 " pdb=" N PRO D 918 " pdb=" CA PRO D 918 " ideal model delta sigma weight residual 119.85 125.69 -5.84 1.01e+00 9.80e-01 3.34e+01 angle pdb=" C MET C 917 " pdb=" N PRO C 918 " pdb=" CA PRO C 918 " ideal model delta sigma weight residual 119.85 125.66 -5.81 1.01e+00 9.80e-01 3.31e+01 angle pdb=" C MET B 917 " pdb=" N PRO B 918 " pdb=" CA PRO B 918 " ideal model delta sigma weight residual 119.85 125.65 -5.80 1.01e+00 9.80e-01 3.29e+01 angle pdb=" C ALA C1002 " pdb=" N PRO C1003 " pdb=" CA PRO C1003 " ideal model delta sigma weight residual 119.66 123.10 -3.44 7.20e-01 1.93e+00 2.29e+01 ... (remaining 43063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 17463 15.25 - 30.50: 1381 30.50 - 45.75: 348 45.75 - 61.00: 68 61.00 - 76.26: 16 Dihedral angle restraints: 19276 sinusoidal: 7600 harmonic: 11676 Sorted by residual: dihedral pdb=" N ASN A 921 " pdb=" CA ASN A 921 " pdb=" CB ASN A 921 " pdb=" CG ASN A 921 " ideal model delta sinusoidal sigma weight residual -180.00 -124.90 -55.10 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" N ASN C 921 " pdb=" CA ASN C 921 " pdb=" CB ASN C 921 " pdb=" CG ASN C 921 " ideal model delta sinusoidal sigma weight residual -180.00 -124.92 -55.08 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" N ASN D 921 " pdb=" CA ASN D 921 " pdb=" CB ASN D 921 " pdb=" CG ASN D 921 " ideal model delta sinusoidal sigma weight residual -180.00 -124.94 -55.06 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 19273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4564 0.060 - 0.119: 536 0.119 - 0.179: 16 0.179 - 0.238: 8 0.238 - 0.298: 12 Chirality restraints: 5136 Sorted by residual: chirality pdb=" C41 YUY A1503 " pdb=" C40 YUY A1503 " pdb=" C42 YUY A1503 " pdb=" O7 YUY A1503 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C41 YUY D3001 " pdb=" C40 YUY D3001 " pdb=" C42 YUY D3001 " pdb=" O7 YUY D3001 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C41 YUY C1503 " pdb=" C40 YUY C1503 " pdb=" C42 YUY C1503 " pdb=" O7 YUY C1503 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 5133 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 760 " 0.033 2.00e-02 2.50e+03 3.64e-02 3.32e+01 pdb=" CG TRP C 760 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP C 760 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TRP C 760 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 760 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP C 760 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 760 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 760 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 760 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP C 760 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 760 " 0.033 2.00e-02 2.50e+03 3.64e-02 3.32e+01 pdb=" CG TRP B 760 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP B 760 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TRP B 760 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 760 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 760 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 760 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 760 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 760 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 760 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 760 " 0.033 2.00e-02 2.50e+03 3.64e-02 3.31e+01 pdb=" CG TRP A 760 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP A 760 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TRP A 760 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 760 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 760 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 760 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 760 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 760 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 760 " 0.005 2.00e-02 2.50e+03 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 192 2.60 - 3.18: 26777 3.18 - 3.75: 49820 3.75 - 4.33: 65496 4.33 - 4.90: 110699 Nonbonded interactions: 252984 Sorted by model distance: nonbonded pdb=" O MET B 917 " pdb=" O8 YUY B1503 " model vdw 2.028 2.440 nonbonded pdb=" O MET C 917 " pdb=" O8 YUY C1503 " model vdw 2.042 2.440 nonbonded pdb=" O MET D 917 " pdb=" O8 YUY D3001 " model vdw 2.044 2.440 nonbonded pdb=" O MET A 917 " pdb=" O8 YUY A1503 " model vdw 2.059 2.440 nonbonded pdb=" O GLN B 138 " pdb=" OH TYR B 154 " model vdw 2.265 2.440 ... (remaining 252979 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 16 through 1092) selection = (chain 'B' and resid 16 through 1092) selection = (chain 'C' and resid 16 through 1092) selection = (chain 'D' and resid 16 through 1092) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 7.490 Check model and map are aligned: 0.450 Set scattering table: 0.300 Process input model: 79.910 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.140 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:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.003 0.034 31512 Z= 0.202 Angle : 0.564 7.340 43068 Z= 0.330 Chirality : 0.040 0.298 5136 Planarity : 0.005 0.054 5260 Dihedral : 12.164 76.256 11676 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Rotamer: Outliers : 0.30 % Allowed : 1.45 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.88 (0.14), residues: 3944 helix: 2.11 (0.10), residues: 2628 sheet: -0.78 (0.31), residues: 272 loop : -0.39 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.002 TRP C 760 HIS 0.002 0.000 HIS D 173 PHE 0.012 0.001 PHE C 969 TYR 0.011 0.001 TYR D 989 ARG 0.003 0.000 ARG D1061 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 3.582 Fit side-chains REVERT: A 64 MET cc_start: 0.8288 (mmm) cc_final: 0.7704 (mmt) REVERT: A 136 MET cc_start: 0.8331 (mmp) cc_final: 0.7941 (mmp) REVERT: A 812 MET cc_start: 0.9110 (mmt) cc_final: 0.8782 (mmt) REVERT: A 843 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8038 (mptt) REVERT: B 64 MET cc_start: 0.8300 (mmm) cc_final: 0.7711 (mmt) REVERT: B 136 MET cc_start: 0.8338 (mmp) cc_final: 0.7950 (mmp) REVERT: B 812 MET cc_start: 0.9127 (mmt) cc_final: 0.8805 (mmt) REVERT: B 843 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8034 (mptt) REVERT: C 64 MET cc_start: 0.8301 (mmm) cc_final: 0.7710 (mmt) REVERT: C 136 MET cc_start: 0.8332 (mmp) cc_final: 0.7937 (mmp) REVERT: C 812 MET cc_start: 0.9123 (mmt) cc_final: 0.8796 (mmt) REVERT: C 843 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8045 (mptt) REVERT: D 64 MET cc_start: 0.8360 (mmm) cc_final: 0.7794 (mmt) REVERT: D 136 MET cc_start: 0.8359 (mmp) cc_final: 0.7948 (mmp) REVERT: D 812 MET cc_start: 0.9110 (mmt) cc_final: 0.8771 (mmt) REVERT: D 843 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8035 (mptt) outliers start: 9 outliers final: 0 residues processed: 168 average time/residue: 1.6241 time to fit residues: 320.7316 Evaluate side-chains 132 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 310 optimal weight: 30.0000 chunk 120 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 359 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 ASN ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 HIS B 794 ASN ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 HIS C 794 ASN ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 HIS D 794 ASN ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 31512 Z= 0.543 Angle : 0.621 6.829 43068 Z= 0.323 Chirality : 0.043 0.159 5136 Planarity : 0.005 0.060 5260 Dihedral : 5.388 49.314 5268 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.21 % Allowed : 4.68 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.80 (0.14), residues: 3944 helix: 2.03 (0.10), residues: 2636 sheet: -0.59 (0.33), residues: 240 loop : -0.46 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 760 HIS 0.005 0.001 HIS D 902 PHE 0.031 0.002 PHE A 734 TYR 0.015 0.002 TYR D 941 ARG 0.005 0.001 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 3.670 Fit side-chains REVERT: A 64 MET cc_start: 0.8388 (mmm) cc_final: 0.7796 (mmt) REVERT: A 136 MET cc_start: 0.8465 (mmp) cc_final: 0.8111 (mmp) REVERT: A 370 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8310 (tpp) REVERT: A 843 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8018 (mptt) REVERT: B 64 MET cc_start: 0.8397 (mmm) cc_final: 0.7811 (mmt) REVERT: B 136 MET cc_start: 0.8456 (mmp) cc_final: 0.8100 (mmp) REVERT: B 257 MET cc_start: 0.8791 (mmm) cc_final: 0.8591 (mmm) REVERT: B 370 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8321 (tpp) REVERT: B 843 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8005 (mptt) REVERT: C 64 MET cc_start: 0.8394 (mmm) cc_final: 0.7805 (mmt) REVERT: C 136 MET cc_start: 0.8473 (mmp) cc_final: 0.8117 (mmp) REVERT: C 257 MET cc_start: 0.8799 (mmm) cc_final: 0.8598 (mmm) REVERT: C 370 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8308 (tpp) REVERT: C 843 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8022 (mptt) REVERT: D 64 MET cc_start: 0.8411 (mmm) cc_final: 0.7830 (mmt) REVERT: D 136 MET cc_start: 0.8458 (mmp) cc_final: 0.8107 (mmp) REVERT: D 370 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8317 (tpp) REVERT: D 843 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8011 (mptt) outliers start: 36 outliers final: 8 residues processed: 160 average time/residue: 1.6547 time to fit residues: 310.3340 Evaluate side-chains 148 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 370 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 299 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 360 optimal weight: 0.8980 chunk 389 optimal weight: 20.0000 chunk 320 optimal weight: 7.9990 chunk 357 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 289 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 31512 Z= 0.308 Angle : 0.510 6.510 43068 Z= 0.267 Chirality : 0.038 0.156 5136 Planarity : 0.004 0.057 5260 Dihedral : 5.099 46.025 5268 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.87 % Allowed : 7.81 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.00 (0.14), residues: 3944 helix: 2.21 (0.10), residues: 2636 sheet: -0.61 (0.31), residues: 268 loop : -0.45 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 760 HIS 0.003 0.001 HIS A 115 PHE 0.015 0.001 PHE C 734 TYR 0.013 0.001 TYR B 559 ARG 0.002 0.000 ARG C1080 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 3.509 Fit side-chains REVERT: A 64 MET cc_start: 0.8432 (mmm) cc_final: 0.7802 (mmt) REVERT: A 136 MET cc_start: 0.8436 (mmp) cc_final: 0.8028 (mmt) REVERT: A 370 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8213 (tpp) REVERT: A 843 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8005 (mptt) REVERT: B 64 MET cc_start: 0.8464 (mmm) cc_final: 0.7852 (mmt) REVERT: B 136 MET cc_start: 0.8459 (mmp) cc_final: 0.8051 (mmt) REVERT: B 370 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8206 (tpp) REVERT: B 843 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8002 (mptt) REVERT: C 64 MET cc_start: 0.8428 (mmm) cc_final: 0.7799 (mmt) REVERT: C 136 MET cc_start: 0.8458 (mmp) cc_final: 0.8044 (mmt) REVERT: C 370 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8212 (tpp) REVERT: C 843 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8007 (mptt) REVERT: D 64 MET cc_start: 0.8440 (mmm) cc_final: 0.7848 (mmt) REVERT: D 136 MET cc_start: 0.8469 (mmp) cc_final: 0.8065 (mmt) REVERT: D 370 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8211 (tpp) REVERT: D 843 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8016 (mptt) outliers start: 26 outliers final: 12 residues processed: 148 average time/residue: 1.5776 time to fit residues: 276.4580 Evaluate side-chains 152 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 370 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 9.9990 chunk 270 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 39 optimal weight: 0.0370 chunk 171 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 361 optimal weight: 4.9990 chunk 382 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 342 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31512 Z= 0.160 Angle : 0.459 6.963 43068 Z= 0.240 Chirality : 0.035 0.152 5136 Planarity : 0.004 0.056 5260 Dihedral : 4.764 44.114 5268 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.24 % Allowed : 8.71 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.25 (0.14), residues: 3944 helix: 2.44 (0.10), residues: 2632 sheet: -0.47 (0.33), residues: 240 loop : -0.47 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 984 HIS 0.002 0.001 HIS D 115 PHE 0.011 0.001 PHE B 828 TYR 0.012 0.001 TYR C 989 ARG 0.002 0.000 ARG B1080 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 3.860 Fit side-chains REVERT: A 64 MET cc_start: 0.8358 (mmm) cc_final: 0.7753 (mmt) REVERT: A 136 MET cc_start: 0.8410 (mmp) cc_final: 0.7955 (mmt) REVERT: A 257 MET cc_start: 0.8792 (mmp) cc_final: 0.8511 (mmm) REVERT: A 812 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8937 (mmm) REVERT: B 64 MET cc_start: 0.8324 (mmm) cc_final: 0.7704 (mmt) REVERT: B 136 MET cc_start: 0.8413 (mmp) cc_final: 0.7955 (mmt) REVERT: B 812 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8946 (mmm) REVERT: C 64 MET cc_start: 0.8366 (mmm) cc_final: 0.7765 (mmt) REVERT: C 136 MET cc_start: 0.8410 (mmp) cc_final: 0.7964 (mmt) REVERT: D 64 MET cc_start: 0.8328 (mmm) cc_final: 0.7712 (mmt) REVERT: D 136 MET cc_start: 0.8419 (mmp) cc_final: 0.7951 (mmt) REVERT: D 257 MET cc_start: 0.8784 (mmp) cc_final: 0.8473 (mmm) outliers start: 37 outliers final: 4 residues processed: 148 average time/residue: 1.5735 time to fit residues: 277.5630 Evaluate side-chains 138 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 812 MET Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain D residue 509 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 7.9990 chunk 217 optimal weight: 0.0470 chunk 5 optimal weight: 10.0000 chunk 285 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 195 optimal weight: 10.0000 chunk 343 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 overall best weight: 4.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 31512 Z= 0.372 Angle : 0.537 7.197 43068 Z= 0.277 Chirality : 0.039 0.149 5136 Planarity : 0.004 0.056 5260 Dihedral : 4.838 44.834 5252 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.01 % Allowed : 9.12 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.21 (0.14), residues: 3944 helix: 2.37 (0.10), residues: 2636 sheet: -0.49 (0.33), residues: 240 loop : -0.38 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 984 HIS 0.003 0.001 HIS B 115 PHE 0.017 0.001 PHE A 734 TYR 0.012 0.002 TYR C 989 ARG 0.002 0.000 ARG C 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 3.394 Fit side-chains REVERT: A 64 MET cc_start: 0.8359 (mmm) cc_final: 0.7724 (mmt) REVERT: A 136 MET cc_start: 0.8451 (mmp) cc_final: 0.7992 (mmt) REVERT: A 190 MET cc_start: 0.9064 (tpp) cc_final: 0.8747 (tpt) REVERT: A 257 MET cc_start: 0.8835 (mmp) cc_final: 0.8547 (mmm) REVERT: A 843 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8034 (mptt) REVERT: B 64 MET cc_start: 0.8361 (mmm) cc_final: 0.7732 (mmt) REVERT: B 136 MET cc_start: 0.8467 (mmp) cc_final: 0.8010 (mmt) REVERT: B 257 MET cc_start: 0.8752 (mmp) cc_final: 0.8476 (mmm) REVERT: B 843 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8021 (mptt) REVERT: C 64 MET cc_start: 0.8364 (mmm) cc_final: 0.7729 (mmt) REVERT: C 136 MET cc_start: 0.8452 (mmp) cc_final: 0.7987 (mmt) REVERT: C 843 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8035 (mptt) REVERT: D 64 MET cc_start: 0.8381 (mmm) cc_final: 0.7751 (mmt) REVERT: D 136 MET cc_start: 0.8450 (mmp) cc_final: 0.7989 (mmt) REVERT: D 257 MET cc_start: 0.8812 (mmp) cc_final: 0.8515 (mmm) REVERT: D 843 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8021 (mptt) outliers start: 30 outliers final: 12 residues processed: 148 average time/residue: 1.5710 time to fit residues: 273.9221 Evaluate side-chains 148 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 9.9990 chunk 344 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 224 optimal weight: 40.0000 chunk 94 optimal weight: 4.9990 chunk 383 optimal weight: 0.9980 chunk 318 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 31512 Z= 0.248 Angle : 0.488 7.423 43068 Z= 0.253 Chirality : 0.037 0.150 5136 Planarity : 0.004 0.056 5260 Dihedral : 4.734 43.694 5252 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.35 % Allowed : 9.39 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.29 (0.14), residues: 3944 helix: 2.46 (0.10), residues: 2632 sheet: -0.47 (0.31), residues: 268 loop : -0.38 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 984 HIS 0.002 0.001 HIS B 115 PHE 0.011 0.001 PHE A 734 TYR 0.012 0.001 TYR C 989 ARG 0.001 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 3.619 Fit side-chains REVERT: A 64 MET cc_start: 0.8384 (mmm) cc_final: 0.7730 (mmt) REVERT: A 136 MET cc_start: 0.8438 (mmp) cc_final: 0.7976 (mmt) REVERT: A 257 MET cc_start: 0.8835 (mmp) cc_final: 0.8516 (mmm) REVERT: A 812 MET cc_start: 0.9249 (mmt) cc_final: 0.8948 (mmm) REVERT: A 843 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8017 (mptt) REVERT: B 64 MET cc_start: 0.8385 (mmm) cc_final: 0.7759 (mmt) REVERT: B 136 MET cc_start: 0.8455 (mmp) cc_final: 0.7993 (mmt) REVERT: B 257 MET cc_start: 0.8828 (mmp) cc_final: 0.8534 (mmm) REVERT: B 812 MET cc_start: 0.9247 (mmt) cc_final: 0.8944 (mmm) REVERT: B 843 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8019 (mptt) REVERT: C 64 MET cc_start: 0.8391 (mmm) cc_final: 0.7734 (mmt) REVERT: C 136 MET cc_start: 0.8437 (mmp) cc_final: 0.7970 (mmt) REVERT: C 812 MET cc_start: 0.9240 (mmt) cc_final: 0.8944 (mmm) REVERT: C 843 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8020 (mptt) REVERT: C 911 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8482 (mt-10) REVERT: D 64 MET cc_start: 0.8385 (mmm) cc_final: 0.7759 (mmt) REVERT: D 136 MET cc_start: 0.8452 (mmp) cc_final: 0.7993 (mmt) REVERT: D 257 MET cc_start: 0.8820 (mmp) cc_final: 0.8496 (mmm) REVERT: D 812 MET cc_start: 0.9249 (mmt) cc_final: 0.8946 (mmm) REVERT: D 843 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8018 (mptt) outliers start: 40 outliers final: 11 residues processed: 163 average time/residue: 1.5820 time to fit residues: 308.3342 Evaluate side-chains 148 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain C residue 911 GLU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 chunk 216 optimal weight: 8.9990 chunk 322 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 381 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 0.0170 chunk 176 optimal weight: 0.9980 overall best weight: 4.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 31512 Z= 0.375 Angle : 0.540 7.989 43068 Z= 0.278 Chirality : 0.038 0.148 5136 Planarity : 0.004 0.056 5260 Dihedral : 4.867 43.978 5252 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.08 % Allowed : 10.20 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.16 (0.14), residues: 3944 helix: 2.37 (0.10), residues: 2636 sheet: -0.75 (0.31), residues: 276 loop : -0.41 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 984 HIS 0.002 0.001 HIS D 115 PHE 0.015 0.001 PHE B 734 TYR 0.012 0.001 TYR C 989 ARG 0.002 0.000 ARG C 887 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 3.296 Fit side-chains REVERT: A 64 MET cc_start: 0.8354 (mmm) cc_final: 0.7724 (mmt) REVERT: A 136 MET cc_start: 0.8580 (mmp) cc_final: 0.8098 (mmt) REVERT: A 257 MET cc_start: 0.8841 (mmp) cc_final: 0.8523 (mmm) REVERT: A 721 MET cc_start: 0.8533 (ttp) cc_final: 0.8242 (ttp) REVERT: A 843 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8004 (mptt) REVERT: B 64 MET cc_start: 0.8360 (mmm) cc_final: 0.7735 (mmt) REVERT: B 136 MET cc_start: 0.8557 (mmp) cc_final: 0.8096 (mmt) REVERT: B 194 MET cc_start: 0.8668 (mmt) cc_final: 0.8273 (mmm) REVERT: B 257 MET cc_start: 0.8850 (mmp) cc_final: 0.8531 (mmm) REVERT: B 721 MET cc_start: 0.8533 (ttp) cc_final: 0.8237 (ttp) REVERT: B 843 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8005 (mptt) REVERT: C 64 MET cc_start: 0.8361 (mmm) cc_final: 0.7747 (mmt) REVERT: C 136 MET cc_start: 0.8552 (mmp) cc_final: 0.8091 (mmt) REVERT: C 721 MET cc_start: 0.8531 (ttp) cc_final: 0.8242 (ttp) REVERT: C 843 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8004 (mptt) REVERT: C 911 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: D 64 MET cc_start: 0.8361 (mmm) cc_final: 0.7736 (mmt) REVERT: D 136 MET cc_start: 0.8581 (mmp) cc_final: 0.8099 (mmt) REVERT: D 721 MET cc_start: 0.8532 (ttp) cc_final: 0.8236 (ttp) REVERT: D 843 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8004 (mptt) outliers start: 32 outliers final: 11 residues processed: 156 average time/residue: 1.5961 time to fit residues: 300.2118 Evaluate side-chains 148 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain C residue 911 GLU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 260 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 31512 Z= 0.186 Angle : 0.477 8.213 43068 Z= 0.246 Chirality : 0.036 0.150 5136 Planarity : 0.004 0.056 5260 Dihedral : 4.684 42.613 5252 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.04 % Allowed : 10.36 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.31 (0.14), residues: 3944 helix: 2.49 (0.10), residues: 2624 sheet: -0.53 (0.31), residues: 268 loop : -0.39 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 984 HIS 0.002 0.000 HIS D 115 PHE 0.013 0.001 PHE C 828 TYR 0.012 0.001 TYR B 989 ARG 0.004 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 3.613 Fit side-chains REVERT: A 64 MET cc_start: 0.8364 (mmm) cc_final: 0.7728 (mmt) REVERT: A 136 MET cc_start: 0.8535 (mmp) cc_final: 0.8025 (mmt) REVERT: A 257 MET cc_start: 0.8857 (mmp) cc_final: 0.8517 (mmm) REVERT: A 721 MET cc_start: 0.8476 (ttp) cc_final: 0.8214 (ttp) REVERT: A 843 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8001 (mptt) REVERT: B 64 MET cc_start: 0.8348 (mmm) cc_final: 0.7725 (mmt) REVERT: B 136 MET cc_start: 0.8538 (mmp) cc_final: 0.8027 (mmt) REVERT: B 190 MET cc_start: 0.8905 (tpt) cc_final: 0.8611 (tpt) REVERT: B 257 MET cc_start: 0.8849 (mmp) cc_final: 0.8495 (mmm) REVERT: B 721 MET cc_start: 0.8475 (ttp) cc_final: 0.8212 (ttp) REVERT: B 843 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8000 (mptt) REVERT: C 64 MET cc_start: 0.8354 (mmm) cc_final: 0.7711 (mmt) REVERT: C 136 MET cc_start: 0.8535 (mmp) cc_final: 0.8022 (mmt) REVERT: C 190 MET cc_start: 0.9024 (tpp) cc_final: 0.8760 (tpt) REVERT: C 721 MET cc_start: 0.8476 (ttp) cc_final: 0.8216 (ttp) REVERT: C 843 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8001 (mptt) REVERT: C 911 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: D 64 MET cc_start: 0.8348 (mmm) cc_final: 0.7725 (mmt) REVERT: D 136 MET cc_start: 0.8537 (mmp) cc_final: 0.8026 (mmt) REVERT: D 190 MET cc_start: 0.9079 (tpp) cc_final: 0.8807 (tpt) REVERT: D 257 MET cc_start: 0.8737 (mmm) cc_final: 0.8479 (mmm) REVERT: D 721 MET cc_start: 0.8478 (ttp) cc_final: 0.8214 (ttp) REVERT: D 843 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8000 (mptt) outliers start: 31 outliers final: 12 residues processed: 151 average time/residue: 1.5942 time to fit residues: 285.0303 Evaluate side-chains 146 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain C residue 911 GLU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 779 MET Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 2.9990 chunk 365 optimal weight: 10.0000 chunk 333 optimal weight: 0.8980 chunk 355 optimal weight: 0.4980 chunk 214 optimal weight: 0.4980 chunk 154 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 336 optimal weight: 9.9990 chunk 354 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 31512 Z= 0.159 Angle : 0.470 8.559 43068 Z= 0.239 Chirality : 0.035 0.149 5136 Planarity : 0.004 0.056 5260 Dihedral : 4.542 42.885 5252 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.71 % Allowed : 10.77 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.43 (0.14), residues: 3944 helix: 2.59 (0.10), residues: 2632 sheet: -0.27 (0.34), residues: 240 loop : -0.48 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 984 HIS 0.002 0.000 HIS B 115 PHE 0.011 0.001 PHE D 828 TYR 0.012 0.001 TYR D 989 ARG 0.001 0.000 ARG D 495 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 3.424 Fit side-chains REVERT: A 64 MET cc_start: 0.8351 (mmm) cc_final: 0.7721 (mmt) REVERT: A 136 MET cc_start: 0.8480 (mmp) cc_final: 0.8001 (mmt) REVERT: A 721 MET cc_start: 0.8476 (ttp) cc_final: 0.8259 (ttp) REVERT: A 812 MET cc_start: 0.9228 (mmt) cc_final: 0.8910 (mmt) REVERT: A 843 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.7952 (mptt) REVERT: B 64 MET cc_start: 0.8334 (mmm) cc_final: 0.7711 (mmt) REVERT: B 136 MET cc_start: 0.8491 (mmp) cc_final: 0.8008 (mmt) REVERT: B 190 MET cc_start: 0.8893 (tpt) cc_final: 0.8609 (tpt) REVERT: B 257 MET cc_start: 0.8868 (mmp) cc_final: 0.8534 (mmm) REVERT: B 721 MET cc_start: 0.8476 (ttp) cc_final: 0.8252 (ttp) REVERT: B 812 MET cc_start: 0.9229 (mmt) cc_final: 0.8915 (mmt) REVERT: B 843 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.7941 (mptt) REVERT: C 64 MET cc_start: 0.8363 (mmm) cc_final: 0.7694 (mmt) REVERT: C 136 MET cc_start: 0.8481 (mmp) cc_final: 0.7998 (mmt) REVERT: C 190 MET cc_start: 0.9063 (tpp) cc_final: 0.8820 (tpt) REVERT: C 721 MET cc_start: 0.8479 (ttp) cc_final: 0.8257 (ttp) REVERT: C 812 MET cc_start: 0.9229 (mmt) cc_final: 0.8908 (mmt) REVERT: C 843 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.7941 (mptt) REVERT: D 64 MET cc_start: 0.8334 (mmm) cc_final: 0.7710 (mmt) REVERT: D 136 MET cc_start: 0.8483 (mmp) cc_final: 0.8003 (mmt) REVERT: D 190 MET cc_start: 0.9088 (tpp) cc_final: 0.8845 (tpt) REVERT: D 257 MET cc_start: 0.8782 (mmm) cc_final: 0.8453 (mmm) REVERT: D 721 MET cc_start: 0.8477 (ttp) cc_final: 0.8256 (ttp) REVERT: D 812 MET cc_start: 0.9230 (mmt) cc_final: 0.8909 (mmt) REVERT: D 843 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.7953 (mptt) outliers start: 21 outliers final: 8 residues processed: 153 average time/residue: 1.4984 time to fit residues: 272.2217 Evaluate side-chains 144 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 779 MET Chi-restraints excluded: chain D residue 843 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 9.9990 chunk 376 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 chunk 363 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 chunk 192 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 943 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 31512 Z= 0.273 Angle : 0.515 9.084 43068 Z= 0.261 Chirality : 0.037 0.148 5136 Planarity : 0.004 0.055 5260 Dihedral : 4.620 42.377 5252 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.64 % Allowed : 10.97 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.35 (0.14), residues: 3944 helix: 2.53 (0.10), residues: 2632 sheet: -0.27 (0.34), residues: 240 loop : -0.51 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 984 HIS 0.002 0.001 HIS A 115 PHE 0.013 0.001 PHE B 567 TYR 0.012 0.001 TYR C 989 ARG 0.002 0.000 ARG B1080 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 3.592 Fit side-chains REVERT: A 64 MET cc_start: 0.8364 (mmm) cc_final: 0.7716 (mmt) REVERT: A 136 MET cc_start: 0.8507 (mmp) cc_final: 0.8040 (mmt) REVERT: A 257 MET cc_start: 0.8730 (mmm) cc_final: 0.8434 (mmm) REVERT: A 721 MET cc_start: 0.8522 (ttp) cc_final: 0.8297 (ttp) REVERT: A 843 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.7996 (mptt) REVERT: B 64 MET cc_start: 0.8388 (mmm) cc_final: 0.7774 (mmt) REVERT: B 136 MET cc_start: 0.8516 (mmp) cc_final: 0.8047 (mmt) REVERT: B 257 MET cc_start: 0.8870 (mmp) cc_final: 0.8549 (mmm) REVERT: B 721 MET cc_start: 0.8520 (ttp) cc_final: 0.8297 (ttp) REVERT: B 843 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.7996 (mptt) REVERT: C 64 MET cc_start: 0.8371 (mmm) cc_final: 0.7724 (mmt) REVERT: C 136 MET cc_start: 0.8509 (mmp) cc_final: 0.8039 (mmt) REVERT: C 721 MET cc_start: 0.8523 (ttp) cc_final: 0.8299 (ttp) REVERT: C 843 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.7997 (mptt) REVERT: D 64 MET cc_start: 0.8387 (mmm) cc_final: 0.7773 (mmt) REVERT: D 136 MET cc_start: 0.8507 (mmp) cc_final: 0.8039 (mmt) REVERT: D 190 MET cc_start: 0.9096 (tpp) cc_final: 0.8875 (tpp) REVERT: D 257 MET cc_start: 0.8762 (mmm) cc_final: 0.8459 (mtp) REVERT: D 721 MET cc_start: 0.8523 (ttp) cc_final: 0.8299 (ttp) REVERT: D 843 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.7996 (mptt) outliers start: 19 outliers final: 12 residues processed: 143 average time/residue: 1.6787 time to fit residues: 282.3017 Evaluate side-chains 147 residues out of total 3520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 516 MET Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 779 MET Chi-restraints excluded: chain C residue 843 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 516 MET Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 843 LYS Chi-restraints excluded: chain D residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 3.9990 chunk 334 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 289 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 323 optimal weight: 0.0770 chunk 39 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.052321 restraints weight = 84741.336| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.72 r_work: 0.2742 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31512 Z= 0.147 Angle : 0.470 8.899 43068 Z= 0.239 Chirality : 0.035 0.150 5136 Planarity : 0.004 0.056 5260 Dihedral : 4.475 42.646 5252 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.44 % Allowed : 11.17 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 2.42 (0.14), residues: 3944 helix: 2.61 (0.10), residues: 2628 sheet: -0.60 (0.32), residues: 272 loop : -0.44 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 984 HIS 0.002 0.000 HIS D 115 PHE 0.012 0.001 PHE D 828 TYR 0.012 0.001 TYR C 989 ARG 0.003 0.000 ARG A 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7213.81 seconds wall clock time: 151 minutes 9.59 seconds (9069.59 seconds total)