Starting phenix.real_space_refine on Fri Sep 27 17:26:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z7n_39820/09_2024/8z7n_39820.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z7n_39820/09_2024/8z7n_39820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z7n_39820/09_2024/8z7n_39820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z7n_39820/09_2024/8z7n_39820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z7n_39820/09_2024/8z7n_39820.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z7n_39820/09_2024/8z7n_39820.cif" } resolution = 3.58 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= 0.001 sd= 0.020 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 108 5.16 5 C 10443 2.51 5 N 2859 2.21 5 O 3231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16641 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3019 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 5 Chain: "B" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1070 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "C" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1374 Classifications: {'peptide': 177} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3019 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 5 Chain: "E" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1070 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "F" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1374 Classifications: {'peptide': 177} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3019 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 5 Chain: "H" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1070 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1374 Classifications: {'peptide': 177} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 11.37, per 1000 atoms: 0.68 Number of scatterers: 16641 At special positions: 0 Unit cell: (121.18, 170.15, 186.75, 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 108 16.00 O 3231 8.00 N 2859 7.00 C 10443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 211 " distance=2.04 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 202 " distance=2.07 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 245 " distance=2.00 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 337 " distance=2.05 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 451 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 424 " distance=2.04 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS B 612 " distance=2.19 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS B 611 " distance=2.04 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 161 " distance=2.05 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 211 " distance=2.04 Simple disulfide: pdb=" SG CYS D 132 " - pdb=" SG CYS D 202 " distance=2.07 Simple disulfide: pdb=" SG CYS D 224 " - pdb=" SG CYS D 253 " distance=2.02 Simple disulfide: pdb=" SG CYS D 234 " - pdb=" SG CYS D 245 " distance=2.00 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 337 " distance=2.05 Simple disulfide: pdb=" SG CYS D 384 " - pdb=" SG CYS D 451 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 424 " distance=2.04 Simple disulfide: pdb=" SG CYS E 605 " - pdb=" SG CYS E 611 " distance=2.04 Simple disulfide: pdb=" SG CYS F 18 " - pdb=" SG CYS F 86 " distance=2.03 Simple disulfide: pdb=" SG CYS F 132 " - pdb=" SG CYS F 161 " distance=2.04 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 80 " distance=2.03 Simple disulfide: pdb=" SG CYS G 125 " - pdb=" SG CYS G 211 " distance=2.04 Simple disulfide: pdb=" SG CYS G 132 " - pdb=" SG CYS G 202 " distance=2.07 Simple disulfide: pdb=" SG CYS G 224 " - pdb=" SG CYS G 253 " distance=2.02 Simple disulfide: pdb=" SG CYS G 234 " - pdb=" SG CYS G 245 " distance=2.00 Simple disulfide: pdb=" SG CYS G 302 " - pdb=" SG CYS G 337 " distance=2.05 Simple disulfide: pdb=" SG CYS G 384 " - pdb=" SG CYS G 451 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 424 " distance=2.04 Simple disulfide: pdb=" SG CYS G 507 " - pdb=" SG CYS H 612 " distance=2.02 Simple disulfide: pdb=" SG CYS H 605 " - pdb=" SG CYS H 611 " distance=2.04 Simple disulfide: pdb=" SG CYS I 18 " - pdb=" SG CYS I 86 " distance=2.03 Simple disulfide: pdb=" SG CYS I 132 " - pdb=" SG CYS I 161 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 94 " " NAG A 602 " - " ASN A 361 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 623 " " NAG B 703 " - " ASN B 632 " " NAG B 704 " - " ASN B 644 " " NAG D 601 " - " ASN D 94 " " NAG D 602 " - " ASN D 361 " " NAG E 701 " - " ASN E 618 " " NAG E 702 " - " ASN E 623 " " NAG E 703 " - " ASN E 632 " " NAG E 704 " - " ASN E 644 " " NAG G 601 " - " ASN G 94 " " NAG G 602 " - " ASN G 361 " " NAG H 701 " - " ASN H 618 " " NAG H 702 " - " ASN H 623 " " NAG H 703 " - " ASN H 632 " " NAG H 704 " - " ASN H 644 " Time building additional restraints: 4.50 Conformation dependent library (CDL) restraints added in 2.0 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 33 sheets defined 22.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 105 through 122 removed outlier: 3.987A pdb=" N ASP A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.302A pdb=" N THR A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'B' and resid 536 through 551 removed outlier: 4.539A pdb=" N THR B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 546 " --> pdb=" O MET B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 600 removed outlier: 4.038A pdb=" N TRP B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG B 586 " --> pdb=" O GLN B 582 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 632 Processing helix chain 'B' and resid 635 through 640 removed outlier: 4.302A pdb=" N LYS B 640 " --> pdb=" O MET B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 645 through 669 removed outlier: 4.145A pdb=" N TYR B 650 " --> pdb=" O THR B 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'D' and resid 70 through 79 Processing helix chain 'D' and resid 105 through 122 removed outlier: 3.988A pdb=" N ASP D 119 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'D' and resid 374 through 379 removed outlier: 4.302A pdb=" N THR D 378 " --> pdb=" O ASP D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 485 Processing helix chain 'E' and resid 536 through 551 removed outlier: 4.538A pdb=" N THR E 545 " --> pdb=" O SER E 541 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL E 546 " --> pdb=" O MET E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 600 removed outlier: 4.038A pdb=" N TRP E 578 " --> pdb=" O GLN E 574 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 584 " --> pdb=" O ILE E 580 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR E 585 " --> pdb=" O LYS E 581 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG E 586 " --> pdb=" O GLN E 582 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 599 " --> pdb=" O LYS E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 632 Processing helix chain 'E' and resid 635 through 640 removed outlier: 4.303A pdb=" N LYS E 640 " --> pdb=" O MET E 636 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 643 No H-bonds generated for 'chain 'E' and resid 641 through 643' Processing helix chain 'E' and resid 645 through 669 removed outlier: 4.144A pdb=" N TYR E 650 " --> pdb=" O THR E 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 67 Processing helix chain 'F' and resid 77 through 81 Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 105 through 122 removed outlier: 3.987A pdb=" N ASP G 119 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN G 120 " --> pdb=" O SER G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 359 Processing helix chain 'G' and resid 374 through 379 removed outlier: 4.302A pdb=" N THR G 378 " --> pdb=" O ASP G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 485 Processing helix chain 'H' and resid 536 through 551 removed outlier: 4.539A pdb=" N THR H 545 " --> pdb=" O SER H 541 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL H 546 " --> pdb=" O MET H 542 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 600 removed outlier: 4.037A pdb=" N TRP H 578 " --> pdb=" O GLN H 574 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN H 584 " --> pdb=" O ILE H 580 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR H 585 " --> pdb=" O LYS H 581 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG H 586 " --> pdb=" O GLN H 582 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 599 " --> pdb=" O LYS H 595 " (cutoff:3.500A) Processing helix chain 'H' and resid 625 through 632 Processing helix chain 'H' and resid 635 through 640 removed outlier: 4.302A pdb=" N LYS H 640 " --> pdb=" O MET H 636 " (cutoff:3.500A) Processing helix chain 'H' and resid 641 through 643 No H-bonds generated for 'chain 'H' and resid 641 through 643' Processing helix chain 'H' and resid 645 through 669 removed outlier: 4.144A pdb=" N TYR H 650 " --> pdb=" O THR H 646 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 67 Processing helix chain 'I' and resid 77 through 81 Processing helix chain 'I' and resid 152 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 390 Processing sheet with id=AA7, first strand: chain 'C' and resid 15 through 18 Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AB1, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.126A pdb=" N LEU C 116 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 148 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.556A pdb=" N CYS C 132 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY C 142 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 41 through 45 Processing sheet with id=AB4, first strand: chain 'D' and resid 59 through 61 Processing sheet with id=AB5, first strand: chain 'D' and resid 126 through 129 Processing sheet with id=AB6, first strand: chain 'D' and resid 230 through 232 Processing sheet with id=AB7, first strand: chain 'D' and resid 290 through 293 Processing sheet with id=AB8, first strand: chain 'D' and resid 389 through 390 Processing sheet with id=AB9, first strand: chain 'F' and resid 15 through 18 Processing sheet with id=AC1, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=AC2, first strand: chain 'F' and resid 82 through 83 Processing sheet with id=AC3, first strand: chain 'F' and resid 102 through 104 removed outlier: 4.125A pdb=" N LEU F 116 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL F 148 " --> pdb=" O LEU F 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 140 through 142 removed outlier: 3.557A pdb=" N CYS F 132 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY F 142 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 41 through 45 Processing sheet with id=AC6, first strand: chain 'G' and resid 59 through 61 Processing sheet with id=AC7, first strand: chain 'G' and resid 126 through 129 Processing sheet with id=AC8, first strand: chain 'G' and resid 230 through 232 Processing sheet with id=AC9, first strand: chain 'G' and resid 290 through 293 Processing sheet with id=AD1, first strand: chain 'G' and resid 389 through 390 Processing sheet with id=AD2, first strand: chain 'I' and resid 15 through 18 Processing sheet with id=AD3, first strand: chain 'I' and resid 29 through 30 Processing sheet with id=AD4, first strand: chain 'I' and resid 82 through 83 Processing sheet with id=AD5, first strand: chain 'I' and resid 102 through 104 removed outlier: 4.125A pdb=" N LEU I 116 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL I 148 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 140 through 142 removed outlier: 3.556A pdb=" N CYS I 132 " --> pdb=" O ILE I 140 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY I 142 " --> pdb=" O VAL I 130 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1017 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: 4.24 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5416 1.34 - 1.47: 4069 1.47 - 1.61: 7318 1.61 - 1.74: 0 1.74 - 1.87: 141 Bond restraints: 16944 Sorted by residual: bond pdb=" C LYS D 498 " pdb=" N PRO D 499 " ideal model delta sigma weight residual 1.337 1.299 0.037 9.80e-03 1.04e+04 1.45e+01 bond pdb=" C LYS A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.337 1.300 0.037 9.80e-03 1.04e+04 1.43e+01 bond pdb=" C LYS G 498 " pdb=" N PRO G 499 " ideal model delta sigma weight residual 1.337 1.300 0.037 9.80e-03 1.04e+04 1.39e+01 bond pdb=" CG1 ILE G 276 " pdb=" CD1 ILE G 276 " ideal model delta sigma weight residual 1.513 1.404 0.109 3.90e-02 6.57e+02 7.76e+00 bond pdb=" CG1 ILE D 276 " pdb=" CD1 ILE D 276 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.69e+00 ... (remaining 16939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 22149 3.22 - 6.44: 709 6.44 - 9.66: 89 9.66 - 12.89: 21 12.89 - 16.11: 6 Bond angle restraints: 22974 Sorted by residual: angle pdb=" N MET A 402 " pdb=" CA MET A 402 " pdb=" C MET A 402 " ideal model delta sigma weight residual 109.81 93.70 16.11 2.21e+00 2.05e-01 5.31e+01 angle pdb=" N MET D 402 " pdb=" CA MET D 402 " pdb=" C MET D 402 " ideal model delta sigma weight residual 109.81 93.71 16.10 2.21e+00 2.05e-01 5.31e+01 angle pdb=" N MET G 402 " pdb=" CA MET G 402 " pdb=" C MET G 402 " ideal model delta sigma weight residual 109.81 93.73 16.08 2.21e+00 2.05e-01 5.30e+01 angle pdb=" N ILE I 36 " pdb=" CA ILE I 36 " pdb=" C ILE I 36 " ideal model delta sigma weight residual 110.05 103.42 6.63 1.09e+00 8.42e-01 3.70e+01 angle pdb=" N ILE F 36 " pdb=" CA ILE F 36 " pdb=" C ILE F 36 " ideal model delta sigma weight residual 110.05 103.44 6.61 1.09e+00 8.42e-01 3.68e+01 ... (remaining 22969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 8321 17.71 - 35.42: 1293 35.42 - 53.13: 672 53.13 - 70.84: 197 70.84 - 88.55: 35 Dihedral angle restraints: 10518 sinusoidal: 4494 harmonic: 6024 Sorted by residual: dihedral pdb=" CB CYS A 507 " pdb=" SG CYS A 507 " pdb=" SG CYS B 612 " pdb=" CB CYS B 612 " ideal model delta sinusoidal sigma weight residual 93.00 8.88 84.12 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS G 507 " pdb=" SG CYS G 507 " pdb=" SG CYS H 612 " pdb=" CB CYS H 612 " ideal model delta sinusoidal sigma weight residual 93.00 11.35 81.65 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CA THR B 634 " pdb=" C THR B 634 " pdb=" N TRP B 635 " pdb=" CA TRP B 635 " ideal model delta harmonic sigma weight residual -180.00 -144.73 -35.27 0 5.00e+00 4.00e-02 4.98e+01 ... (remaining 10515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 2604 0.141 - 0.282: 87 0.282 - 0.423: 11 0.423 - 0.564: 0 0.564 - 0.706: 1 Chirality restraints: 2703 Sorted by residual: chirality pdb=" C1 NAG D 601 " pdb=" ND2 ASN D 94 " pdb=" C2 NAG D 601 " pdb=" O5 NAG D 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CB ILE G 300 " pdb=" CA ILE G 300 " pdb=" CG1 ILE G 300 " pdb=" CG2 ILE G 300 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB ILE D 300 " pdb=" CA ILE D 300 " pdb=" CG1 ILE D 300 " pdb=" CG2 ILE D 300 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2700 not shown) Planarity restraints: 2907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 402 " -0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO A 403 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 403 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 403 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 402 " -0.064 5.00e-02 4.00e+02 9.60e-02 1.47e+01 pdb=" N PRO D 403 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 403 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 403 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET G 402 " -0.064 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO G 403 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO G 403 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 403 " -0.053 5.00e-02 4.00e+02 ... (remaining 2904 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 309 2.46 - 3.07: 12799 3.07 - 3.68: 26840 3.68 - 4.29: 38049 4.29 - 4.90: 59307 Nonbonded interactions: 137304 Sorted by model distance: nonbonded pdb=" OG1 THR D 96 " pdb=" OE1 GLN E 637 " model vdw 1.848 3.040 nonbonded pdb=" OH TYR E 593 " pdb=" OE1 GLN H 598 " model vdw 1.918 3.040 nonbonded pdb=" OE2 GLU D 97 " pdb=" NZ LYS E 640 " model vdw 1.954 3.120 nonbonded pdb=" N TYR A 223 " pdb=" OG1 THR A 254 " model vdw 1.999 3.120 nonbonded pdb=" N TYR G 223 " pdb=" OG1 THR G 254 " model vdw 1.999 3.120 ... (remaining 137299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.660 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4981 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 : 0.010 0.109 16944 Z= 0.644 Angle : 1.353 16.108 22974 Z= 0.727 Chirality : 0.065 0.706 2703 Planarity : 0.008 0.096 2889 Dihedral : 22.405 88.548 6501 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 53.22 Ramachandran Plot: Outliers : 0.74 % Allowed : 22.60 % Favored : 76.67 % Rotamer: Outliers : 29.65 % Allowed : 20.03 % Favored : 50.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.76 % 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: -5.94 (0.14), residues: 2040 helix: -2.98 (0.21), residues: 345 sheet: -3.68 (0.23), residues: 345 loop : -4.62 (0.13), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP H 635 HIS 0.008 0.002 HIS C 29 PHE 0.019 0.004 PHE G 397 TYR 0.032 0.003 TYR G 223 ARG 0.012 0.002 ARG G 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 555 poor density : 277 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.6290 (t0) cc_final: 0.5927 (t0) REVERT: A 67 TYR cc_start: 0.4957 (OUTLIER) cc_final: 0.4608 (t80) REVERT: A 86 SER cc_start: 0.3964 (OUTLIER) cc_final: 0.3584 (t) REVERT: A 97 GLU cc_start: 0.3817 (tp30) cc_final: 0.3616 (mm-30) REVERT: A 136 GLU cc_start: 0.5369 (OUTLIER) cc_final: 0.5031 (tm-30) REVERT: A 137 CYS cc_start: 0.2946 (OUTLIER) cc_final: 0.2004 (t) REVERT: A 266 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6569 (pt) REVERT: A 314 ARG cc_start: 0.0306 (OUTLIER) cc_final: -0.2090 (tpp-160) REVERT: A 341 LYS cc_start: 0.5989 (OUTLIER) cc_final: 0.5567 (mttt) REVERT: A 376 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: A 396 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5429 (tp) REVERT: A 424 CYS cc_start: 0.2083 (OUTLIER) cc_final: 0.0932 (p) REVERT: A 426 ILE cc_start: 0.4801 (OUTLIER) cc_final: 0.4541 (pt) REVERT: A 429 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7871 (mp) REVERT: A 440 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6183 (mmt) REVERT: B 627 LYS cc_start: 0.6839 (mtmm) cc_final: 0.6473 (ptmm) REVERT: B 646 THR cc_start: 0.4148 (OUTLIER) cc_final: 0.3944 (m) REVERT: B 663 ASN cc_start: 0.3918 (OUTLIER) cc_final: 0.3480 (m-40) REVERT: C 13 THR cc_start: 0.7084 (m) cc_final: 0.6879 (m) REVERT: C 97 LEU cc_start: 0.5374 (OUTLIER) cc_final: 0.5114 (tp) REVERT: C 109 HIS cc_start: 0.1733 (OUTLIER) cc_final: 0.0787 (m170) REVERT: C 145 THR cc_start: 0.7407 (OUTLIER) cc_final: 0.6931 (p) REVERT: C 152 GLU cc_start: 0.3739 (OUTLIER) cc_final: 0.3405 (mm-30) REVERT: D 303 THR cc_start: 0.2185 (OUTLIER) cc_final: 0.1509 (m) REVERT: D 304 ARG cc_start: 0.2699 (OUTLIER) cc_final: 0.2037 (tpt90) REVERT: D 341 LYS cc_start: 0.0336 (OUTLIER) cc_final: -0.0199 (ptpp) REVERT: D 425 ARG cc_start: 0.3052 (ptm-80) cc_final: 0.1422 (ptt-90) REVERT: D 430 ILE cc_start: -0.1325 (OUTLIER) cc_final: -0.1580 (pt) REVERT: E 542 MET cc_start: 0.7328 (mmt) cc_final: 0.7108 (mmm) REVERT: E 646 THR cc_start: 0.3467 (OUTLIER) cc_final: 0.3137 (m) REVERT: E 664 GLU cc_start: 0.1168 (OUTLIER) cc_final: -0.1027 (tp30) REVERT: F 26 ILE cc_start: -0.1344 (OUTLIER) cc_final: -0.1916 (mm) REVERT: F 36 ILE cc_start: -0.0637 (OUTLIER) cc_final: -0.1396 (mm) REVERT: F 52 LYS cc_start: -0.3091 (OUTLIER) cc_final: -0.4962 (mmmt) REVERT: F 100 PHE cc_start: -0.0578 (OUTLIER) cc_final: -0.1796 (p90) REVERT: F 159 TRP cc_start: 0.6645 (m-10) cc_final: 0.5847 (m100) REVERT: F 162 THR cc_start: 0.3230 (OUTLIER) cc_final: 0.2901 (m) REVERT: F 171 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5946 (mm-30) REVERT: G 52 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.6024 (tttp) REVERT: G 200 ILE cc_start: -0.1787 (OUTLIER) cc_final: -0.2163 (mt) REVERT: G 266 LEU cc_start: 0.4343 (OUTLIER) cc_final: 0.3807 (tp) REVERT: G 280 SER cc_start: 0.1819 (OUTLIER) cc_final: 0.1368 (t) REVERT: G 288 LYS cc_start: 0.3077 (OUTLIER) cc_final: 0.1825 (mmtm) REVERT: G 294 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6305 (tt) REVERT: G 304 ARG cc_start: 0.5090 (OUTLIER) cc_final: 0.4509 (mmm160) REVERT: G 369 SER cc_start: 0.1478 (OUTLIER) cc_final: 0.0218 (t) REVERT: G 389 PHE cc_start: 0.2763 (m-80) cc_final: 0.2558 (m-10) REVERT: G 396 LEU cc_start: 0.2334 (OUTLIER) cc_final: 0.2075 (tp) REVERT: G 424 CYS cc_start: 0.1689 (OUTLIER) cc_final: 0.0829 (m) REVERT: H 537 MET cc_start: 0.1507 (mtt) cc_final: 0.1010 (mtt) REVERT: H 542 MET cc_start: 0.5273 (mmt) cc_final: 0.4884 (mmm) REVERT: H 664 GLU cc_start: 0.4843 (OUTLIER) cc_final: 0.3643 (tp30) REVERT: I 17 THR cc_start: 0.6126 (OUTLIER) cc_final: 0.5798 (p) REVERT: I 34 ASN cc_start: 0.5977 (OUTLIER) cc_final: 0.5421 (p0) REVERT: I 44 SER cc_start: 0.2682 (OUTLIER) cc_final: 0.2359 (p) REVERT: I 47 THR cc_start: 0.0443 (OUTLIER) cc_final: 0.0221 (p) REVERT: I 100 PHE cc_start: 0.4084 (OUTLIER) cc_final: 0.2432 (p90) REVERT: I 109 HIS cc_start: -0.3427 (OUTLIER) cc_final: -0.4671 (t70) REVERT: I 119 THR cc_start: 0.1655 (OUTLIER) cc_final: 0.1390 (t) REVERT: I 129 SER cc_start: 0.3708 (OUTLIER) cc_final: 0.3495 (p) REVERT: I 144 LYS cc_start: 0.0491 (OUTLIER) cc_final: -0.0096 (mppt) REVERT: I 160 THR cc_start: 0.6843 (OUTLIER) cc_final: 0.6016 (p) REVERT: I 163 VAL cc_start: 0.5216 (OUTLIER) cc_final: 0.4520 (p) REVERT: I 171 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6201 (tp30) REVERT: I 172 PHE cc_start: 0.7063 (m-80) cc_final: 0.6736 (t80) outliers start: 555 outliers final: 130 residues processed: 754 average time/residue: 0.2647 time to fit residues: 301.6326 Evaluate side-chains 361 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 177 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 293 HIS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 304 ARG Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 341 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 546 VAL Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 593 TYR Chi-restraints excluded: chain E residue 600 LEU Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 651 LYS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain E residue 664 GLU Chi-restraints excluded: chain E residue 667 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 52 LYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 211 CYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ARG Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 369 SER Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 424 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 462 ARG Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 546 VAL Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 587 VAL Chi-restraints excluded: chain H residue 597 GLN Chi-restraints excluded: chain H residue 600 LEU Chi-restraints excluded: chain H residue 605 CYS Chi-restraints excluded: chain H residue 643 SER Chi-restraints excluded: chain H residue 646 THR Chi-restraints excluded: chain H residue 653 LEU Chi-restraints excluded: chain H residue 664 GLU Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 31 LYS Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 100 PHE Chi-restraints excluded: chain I residue 109 HIS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 144 LYS Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 171 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 0.0370 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN A 307 ASN A 454 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 131 GLN D 104 ASN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 ASN F 41 ASN ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 484 ASN ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN I 41 ASN I 167 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4847 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16944 Z= 0.285 Angle : 0.993 12.724 22974 Z= 0.501 Chirality : 0.056 0.520 2703 Planarity : 0.006 0.068 2889 Dihedral : 13.180 95.649 2891 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.12 % Favored : 85.83 % Rotamer: Outliers : 10.79 % Allowed : 27.08 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.15), residues: 2040 helix: -1.49 (0.26), residues: 306 sheet: -3.48 (0.20), residues: 396 loop : -3.78 (0.14), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 159 HIS 0.012 0.001 HIS D 358 PHE 0.035 0.002 PHE G 59 TYR 0.026 0.003 TYR A 223 ARG 0.005 0.001 ARG D 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 204 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 CYS cc_start: 0.6391 (OUTLIER) cc_final: 0.5842 (m) REVERT: A 313 ILE cc_start: -0.2405 (OUTLIER) cc_final: -0.3506 (pt) REVERT: A 314 ARG cc_start: 0.0351 (OUTLIER) cc_final: -0.2064 (tpm170) REVERT: A 344 TRP cc_start: 0.4406 (t60) cc_final: 0.3781 (t-100) REVERT: A 498 LYS cc_start: 0.7083 (tttt) cc_final: 0.6862 (tptt) REVERT: B 537 MET cc_start: 0.5887 (mtt) cc_final: 0.4740 (ttm) REVERT: B 627 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7116 (pttp) REVERT: B 646 THR cc_start: 0.4323 (OUTLIER) cc_final: 0.3842 (m) REVERT: C 145 THR cc_start: 0.7124 (OUTLIER) cc_final: 0.6615 (p) REVERT: D 199 LEU cc_start: 0.6849 (pt) cc_final: 0.6515 (pp) REVERT: D 278 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6765 (tt) REVERT: D 314 ARG cc_start: -0.2142 (OUTLIER) cc_final: -0.3466 (tpt90) REVERT: D 425 ARG cc_start: 0.3208 (ptm-80) cc_final: 0.2041 (ptt-90) REVERT: E 575 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5502 (pp) REVERT: F 36 ILE cc_start: -0.2311 (OUTLIER) cc_final: -0.2809 (mm) REVERT: G 45 TYR cc_start: 0.5610 (OUTLIER) cc_final: 0.5316 (p90) REVERT: G 52 LYS cc_start: 0.6307 (OUTLIER) cc_final: 0.5974 (tptp) REVERT: G 78 HIS cc_start: 0.6256 (t70) cc_final: 0.5794 (t70) REVERT: G 136 GLU cc_start: 0.0982 (OUTLIER) cc_final: -0.0226 (tm-30) REVERT: G 266 LEU cc_start: 0.4552 (OUTLIER) cc_final: 0.4199 (tp) REVERT: G 280 SER cc_start: 0.1510 (OUTLIER) cc_final: 0.1165 (t) REVERT: G 288 LYS cc_start: 0.2606 (OUTLIER) cc_final: 0.1671 (mmtm) REVERT: G 424 CYS cc_start: 0.1616 (OUTLIER) cc_final: 0.1101 (t) REVERT: H 537 MET cc_start: 0.0512 (mtt) cc_final: -0.0968 (mtt) REVERT: H 651 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7083 (tmmt) REVERT: I 94 GLU cc_start: 0.1137 (OUTLIER) cc_final: 0.0737 (tt0) REVERT: I 130 VAL cc_start: 0.6750 (t) cc_final: 0.6507 (t) REVERT: I 155 ASP cc_start: 0.7086 (t70) cc_final: 0.6837 (t70) REVERT: I 162 THR cc_start: -0.4528 (OUTLIER) cc_final: -0.4877 (p) outliers start: 202 outliers final: 86 residues processed: 383 average time/residue: 0.2860 time to fit residues: 166.1617 Evaluate side-chains 262 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 156 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 407 TYR Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 575 LEU Chi-restraints excluded: chain E residue 578 TRP Chi-restraints excluded: chain E residue 593 TYR Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ARG Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 424 CYS Chi-restraints excluded: chain G residue 462 ARG Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 597 GLN Chi-restraints excluded: chain H residue 605 CYS Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 646 THR Chi-restraints excluded: chain H residue 651 LYS Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 597 GLN ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS C 35 GLN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 HIS D 454 ASN D 474 ASN D 484 ASN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 HIS G 380 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 658 ASN ** I 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 GLN I 167 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5248 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 16944 Z= 0.447 Angle : 1.044 14.600 22974 Z= 0.534 Chirality : 0.057 0.420 2703 Planarity : 0.007 0.076 2889 Dihedral : 11.513 112.670 2670 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 30.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 16.37 % Favored : 83.48 % Rotamer: Outliers : 8.71 % Allowed : 28.58 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.55 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.16), residues: 2040 helix: -1.47 (0.24), residues: 345 sheet: -3.09 (0.22), residues: 381 loop : -3.62 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP I 159 HIS 0.017 0.002 HIS A 336 PHE 0.030 0.003 PHE G 59 TYR 0.054 0.004 TYR A 223 ARG 0.015 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 173 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.6056 (mt) REVERT: A 233 LYS cc_start: 0.5145 (OUTLIER) cc_final: 0.4670 (tttt) REVERT: A 424 CYS cc_start: 0.2753 (OUTLIER) cc_final: 0.2366 (p) REVERT: A 455 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.5715 (mp) REVERT: A 498 LYS cc_start: 0.7599 (tttt) cc_final: 0.7300 (tptt) REVERT: B 627 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7008 (ptmm) REVERT: C 145 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.6690 (p) REVERT: C 159 TRP cc_start: 0.6431 (m100) cc_final: 0.6149 (m100) REVERT: D 199 LEU cc_start: 0.7139 (pt) cc_final: 0.6920 (mp) REVERT: D 278 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6680 (pt) REVERT: D 385 ARG cc_start: 0.2613 (mmp-170) cc_final: 0.2173 (mpt180) REVERT: F 36 ILE cc_start: -0.2723 (OUTLIER) cc_final: -0.3111 (mm) REVERT: F 172 PHE cc_start: -0.1137 (m-80) cc_final: -0.1415 (m-80) REVERT: G 78 HIS cc_start: 0.6213 (t70) cc_final: 0.5924 (t70) REVERT: G 106 MET cc_start: 0.6957 (ttp) cc_final: 0.6731 (ttp) REVERT: G 136 GLU cc_start: 0.1376 (OUTLIER) cc_final: 0.0429 (tm-30) REVERT: G 266 LEU cc_start: 0.4990 (OUTLIER) cc_final: 0.4558 (tp) REVERT: G 391 CYS cc_start: -0.0471 (OUTLIER) cc_final: -0.1643 (p) REVERT: G 424 CYS cc_start: 0.2059 (OUTLIER) cc_final: 0.0035 (t) REVERT: H 537 MET cc_start: 0.0676 (mtt) cc_final: -0.0319 (mtt) REVERT: H 578 TRP cc_start: 0.3085 (t-100) cc_final: 0.2673 (t-100) outliers start: 163 outliers final: 91 residues processed: 316 average time/residue: 0.2503 time to fit residues: 122.8013 Evaluate side-chains 244 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 141 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 597 GLN Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 407 TYR Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 424 CYS Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 646 THR Chi-restraints excluded: chain H residue 651 LYS Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 177 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 96 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 186 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 176 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN B 547 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 GLN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS G 358 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4989 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16944 Z= 0.232 Angle : 0.838 11.590 22974 Z= 0.424 Chirality : 0.050 0.410 2703 Planarity : 0.005 0.063 2889 Dihedral : 9.891 109.475 2618 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.14 % Favored : 86.76 % Rotamer: Outliers : 7.48 % Allowed : 29.01 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.16), residues: 2040 helix: -0.86 (0.26), residues: 327 sheet: -3.03 (0.22), residues: 390 loop : -3.28 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 159 HIS 0.012 0.001 HIS G 358 PHE 0.026 0.002 PHE G 59 TYR 0.026 0.002 TYR A 223 ARG 0.005 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 174 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.4580 (OUTLIER) cc_final: 0.2526 (mtmm) REVERT: A 250 THR cc_start: 0.6313 (OUTLIER) cc_final: 0.6020 (m) REVERT: A 338 ASN cc_start: 0.6272 (OUTLIER) cc_final: 0.6043 (p0) REVERT: B 537 MET cc_start: 0.5776 (mtt) cc_final: 0.5418 (mtt) REVERT: B 627 LYS cc_start: 0.7412 (mtmm) cc_final: 0.6979 (pttp) REVERT: C 74 LYS cc_start: 0.7563 (pttt) cc_final: 0.7303 (ptpt) REVERT: D 278 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6194 (pt) REVERT: D 385 ARG cc_start: 0.2531 (mmp-170) cc_final: 0.2077 (mpt180) REVERT: D 402 MET cc_start: 0.1035 (mmm) cc_final: 0.0652 (mmm) REVERT: D 509 ARG cc_start: 0.1124 (OUTLIER) cc_final: 0.0215 (mmt180) REVERT: F 26 ILE cc_start: -0.0732 (OUTLIER) cc_final: -0.1496 (mm) REVERT: G 106 MET cc_start: 0.6829 (ttp) cc_final: 0.6581 (ttp) REVERT: G 266 LEU cc_start: 0.4891 (OUTLIER) cc_final: 0.4515 (tp) REVERT: G 391 CYS cc_start: -0.0441 (OUTLIER) cc_final: -0.1483 (p) REVERT: G 424 CYS cc_start: 0.1814 (OUTLIER) cc_final: -0.0004 (t) REVERT: G 432 MET cc_start: 0.2630 (mmm) cc_final: 0.2376 (mmm) REVERT: G 438 ARG cc_start: 0.2953 (OUTLIER) cc_final: 0.2303 (mmm160) REVERT: H 537 MET cc_start: 0.0392 (mtt) cc_final: -0.1156 (mtt) REVERT: I 121 GLU cc_start: 0.4130 (OUTLIER) cc_final: 0.3515 (pm20) outliers start: 140 outliers final: 85 residues processed: 296 average time/residue: 0.2793 time to fit residues: 125.3838 Evaluate side-chains 245 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 149 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 407 TYR Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 424 CYS Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ARG Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 632 ASN Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 158 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 0.0030 chunk 176 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 550 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 484 ASN ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5077 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16944 Z= 0.262 Angle : 0.838 12.433 22974 Z= 0.425 Chirality : 0.050 0.427 2703 Planarity : 0.005 0.057 2889 Dihedral : 9.562 103.486 2608 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.71 % Favored : 85.25 % Rotamer: Outliers : 7.37 % Allowed : 29.70 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.17), residues: 2040 helix: -0.64 (0.26), residues: 333 sheet: -2.75 (0.23), residues: 411 loop : -3.16 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP I 159 HIS 0.011 0.001 HIS A 255 PHE 0.025 0.002 PHE G 59 TYR 0.040 0.002 TYR A 223 ARG 0.009 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 166 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.4552 (OUTLIER) cc_final: 0.2507 (mtmm) REVERT: B 537 MET cc_start: 0.5685 (mtt) cc_final: 0.5380 (mtt) REVERT: B 627 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6967 (pttp) REVERT: C 109 HIS cc_start: 0.2367 (OUTLIER) cc_final: 0.0805 (m170) REVERT: D 278 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6165 (pt) REVERT: D 385 ARG cc_start: 0.2541 (mmp-170) cc_final: 0.1955 (mpt180) REVERT: D 440 MET cc_start: 0.2176 (tmm) cc_final: -0.0231 (tpt) REVERT: D 445 ILE cc_start: 0.1800 (OUTLIER) cc_final: 0.1452 (mp) REVERT: D 509 ARG cc_start: 0.0785 (OUTLIER) cc_final: 0.0037 (mmt180) REVERT: F 36 ILE cc_start: -0.2527 (mt) cc_final: -0.3338 (mm) REVERT: F 100 PHE cc_start: -0.1410 (OUTLIER) cc_final: -0.1717 (p90) REVERT: G 125 CYS cc_start: 0.1089 (OUTLIER) cc_final: 0.0248 (p) REVERT: G 266 LEU cc_start: 0.5091 (OUTLIER) cc_final: 0.4658 (tp) REVERT: G 391 CYS cc_start: -0.0381 (OUTLIER) cc_final: -0.1528 (p) REVERT: G 424 CYS cc_start: 0.1766 (OUTLIER) cc_final: -0.0015 (t) REVERT: G 438 ARG cc_start: 0.2787 (OUTLIER) cc_final: 0.2283 (mmm160) REVERT: H 542 MET cc_start: 0.5847 (mmm) cc_final: 0.5499 (mmt) REVERT: H 578 TRP cc_start: 0.2925 (t-100) cc_final: 0.2637 (t-100) REVERT: I 5 VAL cc_start: 0.5280 (t) cc_final: 0.4854 (m) REVERT: I 121 GLU cc_start: 0.4197 (OUTLIER) cc_final: 0.3615 (pm20) outliers start: 138 outliers final: 90 residues processed: 281 average time/residue: 0.2852 time to fit residues: 121.9584 Evaluate side-chains 251 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 148 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 344 TRP Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 491 LYS Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 100 PHE Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 279 ARG Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 424 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ARG Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 545 THR Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 629 ILE Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 132 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.0670 chunk 177 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 197 optimal weight: 8.9990 chunk 163 optimal weight: 0.0050 chunk 91 optimal weight: 8.9990 chunk 16 optimal weight: 0.0270 chunk 65 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4888 moved from start: 0.6814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16944 Z= 0.194 Angle : 0.765 10.240 22974 Z= 0.383 Chirality : 0.049 0.450 2703 Planarity : 0.005 0.059 2889 Dihedral : 8.899 100.139 2601 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.01 % Favored : 87.94 % Rotamer: Outliers : 5.77 % Allowed : 30.82 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.17), residues: 2040 helix: -0.52 (0.26), residues: 351 sheet: -2.54 (0.25), residues: 369 loop : -3.05 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 159 HIS 0.007 0.001 HIS A 255 PHE 0.024 0.001 PHE G 59 TYR 0.015 0.001 TYR A 223 ARG 0.003 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 171 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.4333 (OUTLIER) cc_final: 0.2263 (mtmm) REVERT: A 310 ARG cc_start: 0.6016 (mpt180) cc_final: 0.5101 (tpm170) REVERT: A 350 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.4783 (mtt180) REVERT: B 537 MET cc_start: 0.5657 (mtt) cc_final: 0.5345 (mtt) REVERT: B 542 MET cc_start: 0.5323 (mmt) cc_final: 0.5059 (mmp) REVERT: B 627 LYS cc_start: 0.7482 (mtmm) cc_final: 0.7124 (pptt) REVERT: C 74 LYS cc_start: 0.7520 (pttt) cc_final: 0.6787 (tptt) REVERT: C 109 HIS cc_start: 0.2368 (OUTLIER) cc_final: 0.0811 (m170) REVERT: D 304 ARG cc_start: 0.1854 (ptp90) cc_final: -0.0078 (tmt170) REVERT: D 385 ARG cc_start: 0.2605 (mmp-170) cc_final: 0.1896 (mpt180) REVERT: D 402 MET cc_start: 0.0209 (mmm) cc_final: -0.0209 (mmm) REVERT: D 445 ILE cc_start: 0.1531 (OUTLIER) cc_final: 0.1236 (mp) REVERT: D 509 ARG cc_start: 0.0871 (OUTLIER) cc_final: 0.0175 (mmt180) REVERT: F 26 ILE cc_start: -0.0760 (OUTLIER) cc_final: -0.1410 (mm) REVERT: F 36 ILE cc_start: -0.2715 (mt) cc_final: -0.3521 (mm) REVERT: G 266 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4467 (tp) REVERT: G 391 CYS cc_start: -0.0450 (OUTLIER) cc_final: -0.1053 (p) REVERT: G 438 ARG cc_start: 0.2606 (OUTLIER) cc_final: 0.2168 (mmm160) REVERT: I 5 VAL cc_start: 0.5222 (t) cc_final: 0.4761 (m) REVERT: I 121 GLU cc_start: 0.4074 (OUTLIER) cc_final: 0.3634 (pm20) outliers start: 108 outliers final: 68 residues processed: 266 average time/residue: 0.2699 time to fit residues: 107.8828 Evaluate side-chains 227 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 149 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 407 TYR Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 LYS Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 279 ARG Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 132 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 119 optimal weight: 0.3980 chunk 90 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 584 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5099 moved from start: 0.7141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16944 Z= 0.275 Angle : 0.831 11.365 22974 Z= 0.419 Chirality : 0.051 0.493 2703 Planarity : 0.005 0.060 2889 Dihedral : 9.112 97.056 2596 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.12 % Favored : 85.83 % Rotamer: Outliers : 6.30 % Allowed : 30.88 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.17), residues: 2040 helix: -0.49 (0.26), residues: 336 sheet: -2.48 (0.25), residues: 363 loop : -2.97 (0.15), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 41 HIS 0.011 0.001 HIS A 255 PHE 0.022 0.002 PHE G 59 TYR 0.041 0.002 TYR A 223 ARG 0.008 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 155 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.4569 (OUTLIER) cc_final: 0.2478 (mtmm) REVERT: A 310 ARG cc_start: 0.6023 (mpt180) cc_final: 0.5166 (tpm170) REVERT: A 350 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.4908 (mtt180) REVERT: A 453 SER cc_start: 0.7683 (OUTLIER) cc_final: 0.7373 (p) REVERT: A 483 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.6160 (m-30) REVERT: B 537 MET cc_start: 0.5869 (mtt) cc_final: 0.5482 (mtt) REVERT: B 542 MET cc_start: 0.5319 (mmt) cc_final: 0.4995 (mmp) REVERT: B 627 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7087 (pptt) REVERT: C 109 HIS cc_start: 0.2443 (OUTLIER) cc_final: 0.0876 (m170) REVERT: D 385 ARG cc_start: 0.2726 (mmp-170) cc_final: 0.1819 (mpt180) REVERT: D 402 MET cc_start: 0.0145 (mmm) cc_final: -0.0225 (mmm) REVERT: D 445 ILE cc_start: 0.1480 (OUTLIER) cc_final: 0.1179 (mp) REVERT: D 509 ARG cc_start: 0.1105 (OUTLIER) cc_final: 0.0157 (mmt90) REVERT: E 542 MET cc_start: 0.6434 (mmm) cc_final: 0.5431 (mmt) REVERT: F 36 ILE cc_start: -0.2683 (mt) cc_final: -0.3432 (mm) REVERT: F 172 PHE cc_start: -0.2024 (m-80) cc_final: -0.2342 (m-80) REVERT: F 174 ILE cc_start: 0.4210 (OUTLIER) cc_final: 0.3854 (mm) REVERT: G 125 CYS cc_start: 0.1061 (OUTLIER) cc_final: 0.0241 (p) REVERT: G 266 LEU cc_start: 0.5082 (OUTLIER) cc_final: 0.4574 (tp) REVERT: G 391 CYS cc_start: -0.0324 (OUTLIER) cc_final: -0.0893 (p) REVERT: G 438 ARG cc_start: 0.2800 (OUTLIER) cc_final: 0.2182 (mmm160) REVERT: I 5 VAL cc_start: 0.5410 (t) cc_final: 0.4942 (m) REVERT: I 121 GLU cc_start: 0.3957 (OUTLIER) cc_final: 0.3582 (pm20) outliers start: 118 outliers final: 82 residues processed: 256 average time/residue: 0.2898 time to fit residues: 111.1022 Evaluate side-chains 239 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 143 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 CYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 279 ARG Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 623 ASN Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 159 TRP Chi-restraints excluded: chain I residue 178 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 0.0060 chunk 154 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 HIS ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN F 131 GLN F 139 ASN F 165 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5395 moved from start: 0.7799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 16944 Z= 0.507 Angle : 1.050 16.220 22974 Z= 0.538 Chirality : 0.058 0.481 2703 Planarity : 0.007 0.066 2889 Dihedral : 10.118 95.395 2594 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 29.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.57 % Favored : 83.38 % Rotamer: Outliers : 7.21 % Allowed : 30.29 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.16), residues: 2040 helix: -1.11 (0.24), residues: 363 sheet: -2.24 (0.25), residues: 360 loop : -3.38 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP A 41 HIS 0.015 0.002 HIS A 255 PHE 0.020 0.003 PHE G 59 TYR 0.065 0.003 TYR A 223 ARG 0.014 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 151 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.4927 (OUTLIER) cc_final: 0.2668 (mtmm) REVERT: A 310 ARG cc_start: 0.6201 (mpt180) cc_final: 0.5457 (tpm170) REVERT: A 391 CYS cc_start: 0.2232 (OUTLIER) cc_final: -0.0317 (t) REVERT: B 627 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6759 (pttp) REVERT: C 109 HIS cc_start: 0.2504 (OUTLIER) cc_final: 0.0862 (m170) REVERT: D 314 ARG cc_start: -0.0985 (OUTLIER) cc_final: -0.2484 (tpt90) REVERT: D 385 ARG cc_start: 0.2536 (mmp-170) cc_final: 0.1288 (mpt180) REVERT: D 402 MET cc_start: 0.0193 (mmm) cc_final: -0.0087 (mmm) REVERT: D 425 ARG cc_start: 0.3731 (ptm-80) cc_final: 0.1967 (ptt-90) REVERT: D 440 MET cc_start: 0.1909 (tmm) cc_final: 0.1339 (tmm) REVERT: D 445 ILE cc_start: 0.1516 (OUTLIER) cc_final: 0.1214 (mp) REVERT: D 509 ARG cc_start: 0.1900 (OUTLIER) cc_final: 0.1107 (mmt180) REVERT: E 542 MET cc_start: 0.6339 (mmm) cc_final: 0.6122 (mmm) REVERT: F 36 ILE cc_start: -0.2195 (mt) cc_final: -0.2588 (mt) REVERT: F 159 TRP cc_start: 0.4995 (m100) cc_final: 0.4515 (m100) REVERT: G 125 CYS cc_start: 0.1137 (OUTLIER) cc_final: 0.0414 (p) REVERT: G 266 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.4501 (tp) REVERT: G 377 ILE cc_start: 0.5205 (mp) cc_final: 0.4873 (mm) REVERT: G 391 CYS cc_start: -0.0168 (OUTLIER) cc_final: -0.0798 (p) REVERT: G 438 ARG cc_start: 0.3204 (OUTLIER) cc_final: 0.2326 (mmm160) REVERT: I 121 GLU cc_start: 0.4149 (OUTLIER) cc_final: 0.3698 (pm20) outliers start: 135 outliers final: 92 residues processed: 267 average time/residue: 0.2951 time to fit residues: 116.8102 Evaluate side-chains 237 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 133 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 584 GLN Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 CYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 338 ASN Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ARG Chi-restraints excluded: chain H residue 545 THR Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 159 TRP Chi-restraints excluded: chain I residue 178 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 173 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 30.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 ASN ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5152 moved from start: 0.8002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16944 Z= 0.255 Angle : 0.873 16.299 22974 Z= 0.434 Chirality : 0.055 1.052 2703 Planarity : 0.006 0.078 2889 Dihedral : 9.227 93.459 2590 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.33 % Favored : 86.62 % Rotamer: Outliers : 5.24 % Allowed : 31.84 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.17), residues: 2040 helix: -0.62 (0.26), residues: 327 sheet: -2.50 (0.24), residues: 360 loop : -3.03 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 159 HIS 0.009 0.001 HIS A 293 PHE 0.028 0.002 PHE C 172 TYR 0.033 0.002 TYR A 223 ARG 0.006 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 149 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.4666 (OUTLIER) cc_final: 0.2623 (mtmm) REVERT: A 345 HIS cc_start: 0.5490 (OUTLIER) cc_final: 0.4771 (m-70) REVERT: A 350 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.5092 (mtt180) REVERT: A 391 CYS cc_start: 0.1594 (OUTLIER) cc_final: -0.0838 (t) REVERT: B 627 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7076 (pptt) REVERT: C 74 LYS cc_start: 0.7562 (pttt) cc_final: 0.6938 (mttm) REVERT: C 109 HIS cc_start: 0.2022 (OUTLIER) cc_final: 0.0525 (m170) REVERT: C 145 THR cc_start: 0.7292 (m) cc_final: 0.6680 (p) REVERT: D 314 ARG cc_start: -0.1088 (OUTLIER) cc_final: -0.2448 (tpt170) REVERT: D 440 MET cc_start: 0.2014 (tmm) cc_final: 0.1494 (tmm) REVERT: D 445 ILE cc_start: 0.1551 (OUTLIER) cc_final: 0.1058 (mp) REVERT: D 509 ARG cc_start: 0.1471 (OUTLIER) cc_final: 0.0794 (mmt180) REVERT: E 542 MET cc_start: 0.6296 (mmm) cc_final: 0.5351 (mmt) REVERT: F 36 ILE cc_start: -0.2362 (mt) cc_final: -0.2729 (mt) REVERT: F 159 TRP cc_start: 0.4857 (m100) cc_final: 0.4424 (m100) REVERT: G 125 CYS cc_start: 0.1024 (OUTLIER) cc_final: 0.0342 (p) REVERT: G 377 ILE cc_start: 0.5157 (mp) cc_final: 0.4743 (mm) REVERT: G 391 CYS cc_start: 0.0360 (OUTLIER) cc_final: -0.0097 (p) REVERT: G 438 ARG cc_start: 0.3183 (OUTLIER) cc_final: 0.2309 (mmm160) REVERT: I 121 GLU cc_start: 0.3989 (OUTLIER) cc_final: 0.3602 (pm20) outliers start: 98 outliers final: 72 residues processed: 233 average time/residue: 0.2789 time to fit residues: 99.6688 Evaluate side-chains 221 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 136 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 CYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain H residue 629 ILE Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 159 TRP Chi-restraints excluded: chain I residue 178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 203 optimal weight: 0.0870 chunk 187 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 ASN ** E 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN G 285 ASN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5047 moved from start: 0.8209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16944 Z= 0.221 Angle : 0.841 14.509 22974 Z= 0.416 Chirality : 0.050 0.437 2703 Planarity : 0.006 0.067 2889 Dihedral : 8.799 90.655 2587 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.48 % Favored : 86.47 % Rotamer: Outliers : 4.65 % Allowed : 32.59 % Favored : 62.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.17), residues: 2040 helix: -0.73 (0.26), residues: 363 sheet: -2.32 (0.24), residues: 390 loop : -3.04 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 41 HIS 0.008 0.001 HIS A 293 PHE 0.023 0.002 PHE G 59 TYR 0.023 0.002 TYR A 223 ARG 0.014 0.001 ARG G 462 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 142 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.4437 (OUTLIER) cc_final: 0.2294 (mtmm) REVERT: A 345 HIS cc_start: 0.5362 (OUTLIER) cc_final: 0.4833 (m-70) REVERT: A 350 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.4955 (mtt180) REVERT: A 391 CYS cc_start: 0.1515 (OUTLIER) cc_final: -0.0905 (t) REVERT: B 542 MET cc_start: 0.5322 (mmt) cc_final: 0.4998 (mmp) REVERT: B 627 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6914 (pptt) REVERT: C 74 LYS cc_start: 0.7530 (pttt) cc_final: 0.6973 (mttm) REVERT: C 109 HIS cc_start: 0.2165 (OUTLIER) cc_final: 0.0592 (m170) REVERT: C 145 THR cc_start: 0.7360 (m) cc_final: 0.6761 (p) REVERT: D 314 ARG cc_start: -0.1265 (OUTLIER) cc_final: -0.2653 (tpt170) REVERT: D 440 MET cc_start: 0.2202 (tmm) cc_final: 0.1719 (tmm) REVERT: D 445 ILE cc_start: 0.1513 (OUTLIER) cc_final: 0.1013 (mp) REVERT: D 509 ARG cc_start: 0.1414 (OUTLIER) cc_final: 0.0660 (mmt90) REVERT: E 542 MET cc_start: 0.6502 (mmm) cc_final: 0.5587 (mmt) REVERT: F 36 ILE cc_start: -0.2570 (mt) cc_final: -0.2925 (mt) REVERT: F 159 TRP cc_start: 0.4708 (m100) cc_final: 0.4350 (m100) REVERT: G 125 CYS cc_start: 0.0999 (OUTLIER) cc_final: 0.0331 (p) REVERT: G 377 ILE cc_start: 0.5145 (mp) cc_final: 0.4741 (mm) REVERT: G 391 CYS cc_start: 0.0431 (OUTLIER) cc_final: -0.0036 (p) REVERT: G 438 ARG cc_start: 0.3050 (OUTLIER) cc_final: 0.2344 (mmm160) REVERT: I 121 GLU cc_start: 0.3999 (OUTLIER) cc_final: 0.3627 (pm20) outliers start: 87 outliers final: 64 residues processed: 217 average time/residue: 0.2696 time to fit residues: 90.4113 Evaluate side-chains 204 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 127 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 CYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain H residue 629 ILE Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 132 CYS Chi-restraints excluded: chain I residue 178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 142 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.209080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.4852 r_free = 0.4852 target = 0.173466 restraints weight = 46044.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.170764 restraints weight = 38453.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.172525 restraints weight = 32220.994| |-----------------------------------------------------------------------------| r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5184 moved from start: 0.8390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16944 Z= 0.258 Angle : 0.851 15.328 22974 Z= 0.423 Chirality : 0.051 0.416 2703 Planarity : 0.006 0.064 2889 Dihedral : 8.749 87.890 2586 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.07 % Favored : 85.93 % Rotamer: Outliers : 4.49 % Allowed : 32.91 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.17), residues: 2040 helix: -0.65 (0.26), residues: 363 sheet: -2.20 (0.26), residues: 342 loop : -3.01 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 41 HIS 0.009 0.001 HIS A 293 PHE 0.022 0.002 PHE G 59 TYR 0.040 0.002 TYR A 223 ARG 0.008 0.001 ARG G 462 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4070.16 seconds wall clock time: 73 minutes 47.16 seconds (4427.16 seconds total)