Starting phenix.real_space_refine on Sat Jun 14 23:18:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7n_39820/06_2025/8z7n_39820.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7n_39820/06_2025/8z7n_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/cci-nas-00/data/ceres_data/8z7n_39820/06_2025/8z7n_39820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7n_39820/06_2025/8z7n_39820.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7n_39820/06_2025/8z7n_39820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7n_39820/06_2025/8z7n_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-5710/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: 11.06, per 1000 atoms: 0.66 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: 4.96 Conformation dependent library (CDL) restraints added in 2.2 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: 1.78 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: 4.86 Time building geometry restraints manager: 5.50 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: 0.13 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 5.260 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: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.900 Find NCS groups from input model: 0.700 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.970 ------------------------------------------------------------------------------- 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 0.159 16997 Z= 0.454 Angle : 1.382 17.512 23098 Z= 0.735 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01372 ( 18) link_NAG-ASN : angle 4.22051 ( 54) hydrogen bonds : bond 0.22744 ( 405) hydrogen bonds : angle 9.25485 ( 1017) SS BOND : bond 0.03107 ( 35) SS BOND : angle 3.96304 ( 70) covalent geometry : bond 0.00987 (16944) covalent geometry : angle 1.35280 (22974) *********************** 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 to be fit. rotamer outliers: 555 poor density : 277 time to evaluate : 1.883 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: 0.2670 time to fit residues: 305.3627 Evaluate side-chains 361 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 177 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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: 0.0970 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 454 ASN A 484 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 F 112 GLN ** 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 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN I 41 ASN I 167 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5331 r_free = 0.5331 target = 0.215242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.193105 restraints weight = 46259.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.196031 restraints weight = 61638.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.196581 restraints weight = 35283.142| |-----------------------------------------------------------------------------| r_work (final): 0.5098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4129 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16997 Z= 0.195 Angle : 1.025 14.810 23098 Z= 0.506 Chirality : 0.056 0.512 2703 Planarity : 0.006 0.067 2889 Dihedral : 13.074 95.036 2891 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.87 % Favored : 86.08 % Rotamer: Outliers : 11.00 % Allowed : 26.82 % Favored : 62.18 % 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: -4.76 (0.15), residues: 2040 helix: -1.42 (0.26), residues: 306 sheet: -3.45 (0.20), residues: 396 loop : -3.74 (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 0.036 0.002 PHE G 59 TYR 0.023 0.002 TYR A 223 ARG 0.004 0.001 ARG C 133 Details of bonding type rmsd link_NAG-ASN : bond 0.01428 ( 18) link_NAG-ASN : angle 5.25824 ( 54) hydrogen bonds : bond 0.05590 ( 405) hydrogen bonds : angle 7.16996 ( 1017) SS BOND : bond 0.00794 ( 35) SS BOND : angle 2.03273 ( 70) covalent geometry : bond 0.00418 (16944) covalent geometry : angle 0.98942 (22974) *********************** 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 414 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 208 time to evaluate : 2.040 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: A 125 CYS cc_start: 0.6423 (OUTLIER) cc_final: 0.5808 (m) REVERT: A 126 VAL cc_start: 0.6356 (OUTLIER) cc_final: 0.6128 (m) REVERT: A 313 ILE cc_start: -0.2496 (OUTLIER) cc_final: -0.2901 (pt) REVERT: A 314 ARG cc_start: 0.0378 (OUTLIER) cc_final: -0.1989 (tpp-160) REVERT: A 344 TRP cc_start: 0.4358 (t60) cc_final: 0.3771 (t-100) REVERT: A 391 CYS cc_start: 0.0282 (OUTLIER) cc_final: 0.0046 (p) REVERT: A 429 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7610 (mp) REVERT: B 537 MET cc_start: 0.5750 (mtt) cc_final: 0.4817 (ttp) REVERT: B 615 VAL cc_start: -0.1332 (OUTLIER) cc_final: -0.1575 (m) REVERT: B 646 THR cc_start: 0.4432 (OUTLIER) cc_final: 0.3932 (m) REVERT: C 145 THR cc_start: 0.6699 (OUTLIER) cc_final: 0.6208 (p) REVERT: D 199 LEU cc_start: 0.6301 (pt) cc_final: 0.5924 (pp) REVERT: D 314 ARG cc_start: -0.1549 (OUTLIER) cc_final: -0.3240 (tpt90) REVERT: D 425 ARG cc_start: 0.3681 (ptm-80) cc_final: 0.2350 (ptt-90) REVERT: E 575 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5460 (pp) REVERT: E 667 LEU cc_start: 0.3930 (OUTLIER) cc_final: 0.3653 (tp) REVERT: F 36 ILE cc_start: -0.2211 (OUTLIER) cc_final: -0.2657 (mm) REVERT: G 45 TYR cc_start: 0.4978 (OUTLIER) cc_final: 0.4724 (p90) REVERT: G 52 LYS cc_start: 0.6241 (OUTLIER) cc_final: 0.5976 (tptp) REVERT: G 78 HIS cc_start: 0.5886 (t70) cc_final: 0.5494 (t70) REVERT: G 136 GLU cc_start: 0.1156 (OUTLIER) cc_final: -0.0077 (tm-30) REVERT: G 266 LEU cc_start: 0.4491 (OUTLIER) cc_final: 0.4284 (tp) REVERT: G 280 SER cc_start: 0.1352 (OUTLIER) cc_final: 0.1027 (t) REVERT: G 288 LYS cc_start: 0.2752 (OUTLIER) cc_final: 0.1798 (mmtm) REVERT: G 424 CYS cc_start: 0.2135 (OUTLIER) cc_final: 0.1899 (t) REVERT: H 537 MET cc_start: 0.0931 (mtt) cc_final: -0.0338 (mtt) REVERT: I 83 THR cc_start: 0.4736 (OUTLIER) cc_final: 0.4164 (p) REVERT: I 94 GLU cc_start: 0.1184 (OUTLIER) cc_final: 0.0517 (tt0) outliers start: 206 outliers final: 86 residues processed: 388 average time/residue: 0.2785 time to fit residues: 163.0958 Evaluate side-chains 263 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 155 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 125 CYS Chi-restraints excluded: chain A residue 126 VAL 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 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 391 CYS 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 429 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 615 VAL 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 36 ILE 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 225 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 277 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 458 LEU 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 E residue 596 ASP Chi-restraints excluded: chain E residue 667 LEU 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 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 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 I residue 29 HIS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 97 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 133 optimal weight: 0.0000 chunk 119 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 A 285 ASN ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN B 550 GLN B 597 GLN ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS C 35 GLN D 73 ASN D 336 HIS D 454 ASN D 474 ASN ** E 550 GLN ** 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 336 HIS G 380 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 ASN ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5265 r_free = 0.5265 target = 0.209275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.180032 restraints weight = 45749.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.181656 restraints weight = 36512.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.179679 restraints weight = 23447.875| |-----------------------------------------------------------------------------| r_work (final): 0.4894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4811 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16997 Z= 0.244 Angle : 1.000 15.449 23098 Z= 0.498 Chirality : 0.054 0.403 2703 Planarity : 0.006 0.075 2889 Dihedral : 11.274 111.661 2675 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 26.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 15.25 % Favored : 84.61 % Rotamer: Outliers : 8.39 % Allowed : 27.78 % Favored : 63.84 % 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: -4.32 (0.16), residues: 2040 helix: -1.07 (0.26), residues: 327 sheet: -3.15 (0.21), residues: 390 loop : -3.47 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 159 HIS 0.017 0.002 HIS A 336 PHE 0.029 0.003 PHE G 59 TYR 0.045 0.003 TYR A 223 ARG 0.011 0.001 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.01023 ( 18) link_NAG-ASN : angle 5.22505 ( 54) hydrogen bonds : bond 0.05941 ( 405) hydrogen bonds : angle 6.95464 ( 1017) SS BOND : bond 0.00962 ( 35) SS BOND : angle 2.06970 ( 70) covalent geometry : bond 0.00547 (16944) covalent geometry : angle 0.96293 (22974) *********************** 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 337 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 180 time to evaluate : 2.010 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 90 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6387 (pt) REVERT: A 233 LYS cc_start: 0.5203 (OUTLIER) cc_final: 0.4717 (tttt) REVERT: A 396 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.5922 (tp) REVERT: A 455 ILE cc_start: 0.5901 (OUTLIER) cc_final: 0.5541 (mm) REVERT: B 537 MET cc_start: 0.6011 (mtt) cc_final: 0.4797 (ttp) REVERT: B 597 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.5680 (tp-100) REVERT: B 615 VAL cc_start: -0.1271 (OUTLIER) cc_final: -0.1951 (m) REVERT: B 630 TRP cc_start: 0.5691 (m100) cc_final: 0.5348 (m100) REVERT: C 145 THR cc_start: 0.6912 (OUTLIER) cc_final: 0.6311 (p) REVERT: D 509 ARG cc_start: 0.0911 (OUTLIER) cc_final: 0.0063 (mmt180) REVERT: F 36 ILE cc_start: -0.2587 (OUTLIER) cc_final: -0.3098 (mm) REVERT: G 106 MET cc_start: 0.6915 (ttp) cc_final: 0.6687 (ttp) REVERT: G 250 THR cc_start: 0.6738 (OUTLIER) cc_final: 0.6516 (m) REVERT: G 266 LEU cc_start: 0.4763 (OUTLIER) cc_final: 0.4457 (tp) REVERT: G 391 CYS cc_start: -0.0292 (OUTLIER) cc_final: -0.1492 (p) REVERT: G 424 CYS cc_start: 0.2318 (OUTLIER) cc_final: 0.0533 (t) REVERT: H 537 MET cc_start: 0.1130 (mtt) cc_final: -0.0083 (mtt) REVERT: I 5 VAL cc_start: 0.5243 (t) cc_final: 0.4808 (m) REVERT: I 94 GLU cc_start: 0.1646 (OUTLIER) cc_final: 0.1164 (tt0) outliers start: 157 outliers final: 85 residues processed: 317 average time/residue: 0.2563 time to fit residues: 126.9146 Evaluate side-chains 241 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 142 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 125 CYS Chi-restraints excluded: chain A residue 134 THR 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 396 LEU 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 455 ILE 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 597 GLN Chi-restraints excluded: chain B residue 612 CYS Chi-restraints excluded: chain B residue 615 VAL 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 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 39 LEU 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 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 225 THR 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 440 MET 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 585 THR Chi-restraints excluded: chain E residue 588 LEU 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 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 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 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 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 I residue 34 ASN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 178 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 28 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 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 454 ASN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 358 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 GLN I 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5313 r_free = 0.5313 target = 0.212924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.183340 restraints weight = 45582.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.182570 restraints weight = 38283.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.183585 restraints weight = 31285.635| |-----------------------------------------------------------------------------| r_work (final): 0.4934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4641 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16997 Z= 0.158 Angle : 0.858 13.189 23098 Z= 0.425 Chirality : 0.050 0.430 2703 Planarity : 0.005 0.059 2889 Dihedral : 9.715 108.585 2622 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.50 % Favored : 87.40 % Rotamer: Outliers : 6.73 % Allowed : 29.54 % Favored : 63.73 % 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: -3.90 (0.16), residues: 2040 helix: -0.83 (0.25), residues: 342 sheet: -2.80 (0.22), residues: 384 loop : -3.21 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 159 HIS 0.010 0.001 HIS A 380 PHE 0.025 0.002 PHE G 59 TYR 0.020 0.002 TYR A 223 ARG 0.005 0.000 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.00845 ( 18) link_NAG-ASN : angle 4.00595 ( 54) hydrogen bonds : bond 0.04613 ( 405) hydrogen bonds : angle 6.48405 ( 1017) SS BOND : bond 0.00608 ( 35) SS BOND : angle 1.70103 ( 70) covalent geometry : bond 0.00343 (16944) covalent geometry : angle 0.83320 (22974) *********************** 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 292 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 166 time to evaluate : 1.770 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: A 108 ASN cc_start: 0.5357 (m-40) cc_final: 0.5124 (m-40) REVERT: A 250 THR cc_start: 0.6317 (OUTLIER) cc_final: 0.6068 (m) REVERT: A 482 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7132 (mtp180) REVERT: B 537 MET cc_start: 0.5727 (mtt) cc_final: 0.4586 (ttp) REVERT: D 245 CYS cc_start: 0.1178 (OUTLIER) cc_final: -0.0183 (p) REVERT: D 385 ARG cc_start: 0.3077 (mmm160) cc_final: 0.1083 (mmt-90) REVERT: F 26 ILE cc_start: -0.1214 (OUTLIER) cc_final: -0.1717 (mm) REVERT: F 172 PHE cc_start: -0.0759 (m-80) cc_final: -0.1455 (m-80) REVERT: G 266 LEU cc_start: 0.5252 (OUTLIER) cc_final: 0.4811 (tp) REVERT: G 391 CYS cc_start: -0.0580 (OUTLIER) cc_final: -0.1704 (p) REVERT: G 424 CYS cc_start: 0.2126 (OUTLIER) cc_final: 0.0397 (t) REVERT: G 432 MET cc_start: 0.2507 (mmm) cc_final: 0.2245 (mmm) REVERT: I 5 VAL cc_start: 0.5359 (t) cc_final: 0.4907 (m) REVERT: I 94 GLU cc_start: 0.1361 (OUTLIER) cc_final: 0.1042 (tt0) REVERT: I 121 GLU cc_start: 0.3824 (OUTLIER) cc_final: 0.3480 (pm20) outliers start: 126 outliers final: 80 residues processed: 275 average time/residue: 0.2791 time to fit residues: 120.5989 Evaluate side-chains 236 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 148 time to evaluate : 1.862 ------------------------------------------------------------------------------- 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 202 CYS Chi-restraints excluded: chain A residue 225 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 406 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 527 LEU Chi-restraints excluded: chain B residue 544 LEU 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 36 ILE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 VAL 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 90 LEU 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 245 CYS Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 277 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 458 LEU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 586 ARG 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 225 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain G residue 300 ILE 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 459 LEU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 632 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 94 GLU 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 157 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 198 optimal weight: 0.0040 chunk 136 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 307 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 B 626 GLN ** D 264 GLN ** 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 264 GLN ** 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 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5319 r_free = 0.5319 target = 0.213493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.182673 restraints weight = 46319.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.181735 restraints weight = 40720.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.183208 restraints weight = 30664.331| |-----------------------------------------------------------------------------| r_work (final): 0.4921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4679 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16997 Z= 0.147 Angle : 0.817 13.667 23098 Z= 0.404 Chirality : 0.048 0.431 2703 Planarity : 0.005 0.057 2889 Dihedral : 9.007 101.916 2606 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.53 % Favored : 86.42 % Rotamer: Outliers : 6.52 % Allowed : 29.75 % Favored : 63.73 % 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: -3.66 (0.17), residues: 2040 helix: -0.42 (0.26), residues: 333 sheet: -2.70 (0.22), residues: 423 loop : -3.07 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 603 HIS 0.008 0.001 HIS A 255 PHE 0.022 0.002 PHE G 59 TYR 0.021 0.002 TYR A 223 ARG 0.005 0.000 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 18) link_NAG-ASN : angle 4.01324 ( 54) hydrogen bonds : bond 0.04155 ( 405) hydrogen bonds : angle 6.06996 ( 1017) SS BOND : bond 0.00491 ( 35) SS BOND : angle 2.04255 ( 70) covalent geometry : bond 0.00323 (16944) covalent geometry : angle 0.78782 (22974) *********************** 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 279 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 157 time to evaluate : 1.908 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: A 108 ASN cc_start: 0.5333 (m-40) cc_final: 0.5103 (m-40) REVERT: A 123 LYS cc_start: 0.4302 (OUTLIER) cc_final: 0.2198 (mtmm) REVERT: A 125 CYS cc_start: 0.6103 (OUTLIER) cc_final: 0.5658 (m) REVERT: A 338 ASN cc_start: 0.6061 (OUTLIER) cc_final: 0.5837 (p0) REVERT: A 482 ARG cc_start: 0.7690 (mtt90) cc_final: 0.7218 (mtp180) REVERT: B 537 MET cc_start: 0.5693 (mtt) cc_final: 0.4433 (mtt) REVERT: B 581 LYS cc_start: 0.7387 (mmtt) cc_final: 0.6702 (mtpt) REVERT: C 74 LYS cc_start: 0.7381 (pttt) cc_final: 0.6610 (tptt) REVERT: C 109 HIS cc_start: 0.2446 (OUTLIER) cc_final: 0.1014 (m170) REVERT: D 245 CYS cc_start: 0.1467 (OUTLIER) cc_final: -0.0138 (p) REVERT: D 252 GLN cc_start: 0.6269 (tt0) cc_final: 0.5885 (tp40) REVERT: D 385 ARG cc_start: 0.3173 (mmm160) cc_final: 0.1363 (mpt180) REVERT: D 491 LYS cc_start: 0.1651 (OUTLIER) cc_final: 0.1430 (pttm) REVERT: D 509 ARG cc_start: 0.0541 (OUTLIER) cc_final: -0.0191 (mmt180) REVERT: F 26 ILE cc_start: -0.1284 (OUTLIER) cc_final: -0.1821 (mm) REVERT: F 172 PHE cc_start: -0.0987 (m-80) cc_final: -0.1687 (m-80) REVERT: G 266 LEU cc_start: 0.5328 (OUTLIER) cc_final: 0.4870 (tp) REVERT: G 391 CYS cc_start: -0.0461 (OUTLIER) cc_final: -0.1034 (p) REVERT: G 438 ARG cc_start: 0.2489 (OUTLIER) cc_final: 0.2134 (mmm160) REVERT: H 542 MET cc_start: 0.5667 (mmm) cc_final: 0.5316 (mmt) REVERT: H 555 ILE cc_start: 0.0179 (mm) cc_final: -0.0243 (mt) REVERT: I 5 VAL cc_start: 0.5332 (t) cc_final: 0.4857 (m) REVERT: I 94 GLU cc_start: 0.1117 (OUTLIER) cc_final: 0.0812 (tt0) REVERT: I 121 GLU cc_start: 0.3691 (OUTLIER) cc_final: 0.3478 (pm20) outliers start: 122 outliers final: 77 residues processed: 262 average time/residue: 0.2834 time to fit residues: 112.2995 Evaluate side-chains 239 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 149 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 280 SER 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 338 ASN 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 459 LEU 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 527 LEU Chi-restraints excluded: chain B residue 544 LEU 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 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 VAL 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 D residue 45 TYR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 90 LEU 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 245 CYS Chi-restraints excluded: chain D residue 257 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 458 LEU Chi-restraints excluded: chain D residue 491 LYS Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 586 ARG Chi-restraints excluded: chain E residue 643 SER 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 173 LYS 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 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 345 HIS Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 391 CYS 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 575 LEU Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 632 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 94 GLU Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 158 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 0.0970 chunk 198 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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 ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 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 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN D 88 GLN D 307 ASN D 484 ASN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 550 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5215 r_free = 0.5215 target = 0.203840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.172076 restraints weight = 45297.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.170061 restraints weight = 40255.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.171008 restraints weight = 37442.870| |-----------------------------------------------------------------------------| r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5114 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 16997 Z= 0.357 Angle : 1.097 15.150 23098 Z= 0.560 Chirality : 0.058 0.441 2703 Planarity : 0.007 0.102 2889 Dihedral : 10.265 100.334 2598 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 32.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.62 % Favored : 83.38 % Rotamer: Outliers : 7.53 % Allowed : 30.56 % Favored : 61.91 % 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: -4.19 (0.16), residues: 2040 helix: -1.36 (0.24), residues: 357 sheet: -2.71 (0.23), residues: 408 loop : -3.43 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP H 630 HIS 0.013 0.002 HIS A 255 PHE 0.023 0.003 PHE G 59 TYR 0.062 0.004 TYR A 223 ARG 0.015 0.001 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.00991 ( 18) link_NAG-ASN : angle 4.11911 ( 54) hydrogen bonds : bond 0.06733 ( 405) hydrogen bonds : angle 7.08247 ( 1017) SS BOND : bond 0.00985 ( 35) SS BOND : angle 2.56151 ( 70) covalent geometry : bond 0.00828 (16944) covalent geometry : angle 1.07227 (22974) *********************** 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 302 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 161 time to evaluate : 1.680 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 90 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6599 (pt) REVERT: A 108 ASN cc_start: 0.5598 (m-40) cc_final: 0.5256 (m-40) REVERT: A 123 LYS cc_start: 0.4806 (OUTLIER) cc_final: 0.2528 (mtmm) REVERT: A 310 ARG cc_start: 0.5816 (mpt180) cc_final: 0.4937 (tpm170) REVERT: A 401 TYR cc_start: 0.5934 (t80) cc_final: 0.5582 (t80) REVERT: A 483 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6470 (m-30) REVERT: B 537 MET cc_start: 0.5827 (mtt) cc_final: 0.4541 (mtt) REVERT: C 109 HIS cc_start: 0.2437 (OUTLIER) cc_final: 0.0876 (m170) REVERT: D 110 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5783 (mtt) REVERT: D 314 ARG cc_start: -0.0736 (OUTLIER) cc_final: -0.2389 (tpt170) REVERT: D 385 ARG cc_start: 0.3138 (mmm160) cc_final: 0.1377 (mpt180) REVERT: D 425 ARG cc_start: 0.4017 (ptm-80) cc_final: 0.2149 (ptt-90) REVERT: D 445 ILE cc_start: 0.1752 (OUTLIER) cc_final: 0.1442 (mp) REVERT: F 36 ILE cc_start: -0.2392 (mt) cc_final: -0.2785 (mt) REVERT: F 172 PHE cc_start: -0.0541 (m-80) cc_final: -0.1209 (m-80) REVERT: G 266 LEU cc_start: 0.5162 (OUTLIER) cc_final: 0.4593 (tp) REVERT: G 391 CYS cc_start: -0.0378 (OUTLIER) cc_final: -0.1722 (p) REVERT: G 424 CYS cc_start: 0.1798 (OUTLIER) cc_final: -0.0009 (t) REVERT: G 438 ARG cc_start: 0.2798 (OUTLIER) cc_final: 0.2009 (mmm160) REVERT: I 94 GLU cc_start: 0.1199 (OUTLIER) cc_final: 0.0801 (tt0) REVERT: I 121 GLU cc_start: 0.3677 (OUTLIER) cc_final: 0.3407 (pm20) outliers start: 141 outliers final: 98 residues processed: 278 average time/residue: 0.2832 time to fit residues: 117.4768 Evaluate side-chains 251 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 140 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 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 314 ARG 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 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 459 LEU 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 544 LEU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain C residue 6 VAL 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 62 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 VAL 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 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 80 CYS Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 110 MET 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 245 CYS Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 293 HIS 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 404 ASN Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 586 ARG Chi-restraints excluded: chain E residue 588 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 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 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 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 277 ILE Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 297 SER 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 371 SER 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 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 575 LEU 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 94 GLU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 159 TRP Chi-restraints excluded: chain I residue 178 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 12 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 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 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 484 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5268 r_free = 0.5268 target = 0.207400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.174428 restraints weight = 45647.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.170836 restraints weight = 42099.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.172104 restraints weight = 34274.861| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5174 moved from start: 0.7417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 16997 Z= 0.223 Angle : 0.951 20.759 23098 Z= 0.470 Chirality : 0.053 0.515 2703 Planarity : 0.006 0.063 2889 Dihedral : 9.818 99.079 2596 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.46 % Favored : 85.49 % Rotamer: Outliers : 6.89 % Allowed : 31.62 % Favored : 61.49 % 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: -3.86 (0.17), residues: 2040 helix: -0.73 (0.27), residues: 324 sheet: -2.59 (0.23), residues: 390 loop : -3.24 (0.15), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 41 HIS 0.013 0.002 HIS A 255 PHE 0.022 0.002 PHE G 59 TYR 0.051 0.002 TYR A 223 ARG 0.010 0.001 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.01003 ( 18) link_NAG-ASN : angle 5.49175 ( 54) hydrogen bonds : bond 0.05277 ( 405) hydrogen bonds : angle 6.54986 ( 1017) SS BOND : bond 0.00641 ( 35) SS BOND : angle 2.09170 ( 70) covalent geometry : bond 0.00512 (16944) covalent geometry : angle 0.90861 (22974) *********************** 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 277 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 148 time to evaluate : 2.186 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: A 108 ASN cc_start: 0.5513 (m-40) cc_final: 0.5208 (m-40) REVERT: A 123 LYS cc_start: 0.4680 (OUTLIER) cc_final: 0.2495 (mtmm) REVERT: B 537 MET cc_start: 0.5779 (mtt) cc_final: 0.4410 (mtt) REVERT: C 109 HIS cc_start: 0.2173 (OUTLIER) cc_final: 0.0656 (m170) REVERT: D 110 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.5886 (mtt) REVERT: D 314 ARG cc_start: -0.0974 (OUTLIER) cc_final: -0.2476 (tpt170) REVERT: D 385 ARG cc_start: 0.2974 (mmm160) cc_final: 0.1448 (mpt180) REVERT: E 542 MET cc_start: 0.6633 (mmm) cc_final: 0.5861 (mmt) REVERT: F 36 ILE cc_start: -0.2444 (mt) cc_final: -0.2804 (mt) REVERT: F 172 PHE cc_start: -0.0579 (m-80) cc_final: -0.1259 (m-80) REVERT: G 125 CYS cc_start: 0.0418 (OUTLIER) cc_final: -0.0111 (p) REVERT: G 266 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.4825 (tp) REVERT: G 391 CYS cc_start: -0.0371 (OUTLIER) cc_final: -0.1008 (p) REVERT: G 438 ARG cc_start: 0.3079 (OUTLIER) cc_final: 0.2204 (mmm160) REVERT: H 542 MET cc_start: 0.5955 (mmm) cc_final: 0.5700 (mmt) REVERT: I 94 GLU cc_start: 0.0891 (OUTLIER) cc_final: 0.0507 (tt0) REVERT: I 121 GLU cc_start: 0.3912 (OUTLIER) cc_final: 0.3555 (pm20) outliers start: 129 outliers final: 83 residues processed: 262 average time/residue: 0.3356 time to fit residues: 133.3111 Evaluate side-chains 234 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 141 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 204 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 278 ILE 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 363 THR Chi-restraints excluded: chain A residue 400 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 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 544 LEU 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 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 VAL 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 132 CYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 80 CYS Chi-restraints excluded: chain D residue 110 MET 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 293 HIS 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 491 LYS Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 586 ARG 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 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 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 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 297 SER Chi-restraints excluded: chain G residue 300 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 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 496 GLU 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 94 GLU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 GLU 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 187 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.210854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.185562 restraints weight = 45638.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.180901 restraints weight = 45906.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.179451 restraints weight = 36159.350| |-----------------------------------------------------------------------------| r_work (final): 0.4884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4878 moved from start: 0.7774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16997 Z= 0.157 Angle : 0.862 19.994 23098 Z= 0.420 Chirality : 0.050 0.548 2703 Planarity : 0.005 0.062 2889 Dihedral : 9.051 96.200 2596 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.77 % Favored : 86.18 % Rotamer: Outliers : 5.77 % Allowed : 32.59 % Favored : 61.65 % 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: -3.53 (0.17), residues: 2040 helix: -0.36 (0.27), residues: 324 sheet: -2.34 (0.23), residues: 426 loop : -3.06 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 603 HIS 0.010 0.001 HIS A 255 PHE 0.022 0.002 PHE G 59 TYR 0.027 0.002 TYR A 223 ARG 0.005 0.000 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.01053 ( 18) link_NAG-ASN : angle 5.07261 ( 54) hydrogen bonds : bond 0.04228 ( 405) hydrogen bonds : angle 6.05576 ( 1017) SS BOND : bond 0.00542 ( 35) SS BOND : angle 1.63533 ( 70) covalent geometry : bond 0.00346 (16944) covalent geometry : angle 0.82329 (22974) *********************** 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 267 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 159 time to evaluate : 1.901 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 108 ASN cc_start: 0.5286 (m-40) cc_final: 0.5007 (m-40) REVERT: A 123 LYS cc_start: 0.4423 (OUTLIER) cc_final: 0.2311 (mtmm) REVERT: A 345 HIS cc_start: 0.5394 (OUTLIER) cc_final: 0.4858 (m-70) REVERT: A 350 ARG cc_start: 0.6695 (OUTLIER) cc_final: 0.5066 (mtt180) REVERT: B 537 MET cc_start: 0.5448 (mtt) cc_final: 0.4120 (mtt) REVERT: B 542 MET cc_start: 0.4898 (mmt) cc_final: 0.4580 (mmp) REVERT: C 74 LYS cc_start: 0.7517 (pttt) cc_final: 0.6876 (mttm) REVERT: C 109 HIS cc_start: 0.2366 (OUTLIER) cc_final: 0.0791 (m170) REVERT: D 110 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5775 (mtt) REVERT: D 245 CYS cc_start: 0.1567 (OUTLIER) cc_final: -0.0200 (p) REVERT: D 385 ARG cc_start: 0.3119 (mmm160) cc_final: 0.1713 (mpt180) REVERT: D 425 ARG cc_start: 0.3659 (ptm-80) cc_final: 0.1976 (ptt-90) REVERT: D 509 ARG cc_start: 0.2255 (mmp-170) cc_final: 0.1065 (mmt180) REVERT: E 542 MET cc_start: 0.6752 (mmm) cc_final: 0.6049 (mmt) REVERT: F 36 ILE cc_start: -0.2473 (mt) cc_final: -0.2810 (mt) REVERT: F 172 PHE cc_start: -0.0564 (m-80) cc_final: -0.1224 (m-80) REVERT: G 125 CYS cc_start: 0.0850 (OUTLIER) cc_final: 0.0100 (p) REVERT: G 265 LEU cc_start: 0.8510 (mt) cc_final: 0.8297 (mp) REVERT: G 266 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.4512 (tp) REVERT: G 377 ILE cc_start: 0.5337 (mp) cc_final: 0.4897 (mm) REVERT: G 391 CYS cc_start: -0.0300 (OUTLIER) cc_final: -0.0881 (p) REVERT: G 438 ARG cc_start: 0.2951 (OUTLIER) cc_final: 0.2301 (mmm160) REVERT: I 94 GLU cc_start: 0.1275 (OUTLIER) cc_final: 0.0834 (tt0) outliers start: 108 outliers final: 74 residues processed: 254 average time/residue: 0.3218 time to fit residues: 124.6732 Evaluate side-chains 231 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 146 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 204 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 279 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 363 THR Chi-restraints excluded: chain A residue 400 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 462 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL 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 39 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 VAL 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 C residue 132 CYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 110 MET 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 245 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 586 ARG 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 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 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 250 THR 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 297 SER Chi-restraints excluded: chain G residue 300 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 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 496 GLU 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 94 GLU Chi-restraints excluded: chain I residue 119 THR 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 182 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 102 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 184 optimal weight: 0.2980 chunk 147 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 190 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 307 ASN A 334 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN G 285 ASN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5309 r_free = 0.5309 target = 0.210878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.177125 restraints weight = 45506.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.174357 restraints weight = 40269.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.175601 restraints weight = 31370.375| |-----------------------------------------------------------------------------| r_work (final): 0.4827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5039 moved from start: 0.8004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16997 Z= 0.157 Angle : 0.857 19.305 23098 Z= 0.417 Chirality : 0.050 0.508 2703 Planarity : 0.005 0.064 2889 Dihedral : 8.849 93.986 2590 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.14 % Favored : 86.81 % Rotamer: Outliers : 4.86 % Allowed : 33.01 % Favored : 62.13 % 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: -3.36 (0.17), residues: 2040 helix: -0.13 (0.28), residues: 324 sheet: -2.46 (0.24), residues: 390 loop : -2.89 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 603 HIS 0.008 0.001 HIS A 293 PHE 0.021 0.002 PHE G 59 TYR 0.032 0.002 TYR A 223 ARG 0.010 0.001 ARG G 462 Details of bonding type rmsd link_NAG-ASN : bond 0.01017 ( 18) link_NAG-ASN : angle 4.88327 ( 54) hydrogen bonds : bond 0.04167 ( 405) hydrogen bonds : angle 5.99281 ( 1017) SS BOND : bond 0.00500 ( 35) SS BOND : angle 1.84891 ( 70) covalent geometry : bond 0.00352 (16944) covalent geometry : angle 0.81984 (22974) *********************** 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 241 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 150 time to evaluate : 1.838 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 108 ASN cc_start: 0.5466 (m-40) cc_final: 0.5168 (m-40) REVERT: A 123 LYS cc_start: 0.4369 (OUTLIER) cc_final: 0.2269 (mtmm) REVERT: A 304 ARG cc_start: 0.6626 (mtm-85) cc_final: 0.6305 (mpp-170) REVERT: A 345 HIS cc_start: 0.5267 (OUTLIER) cc_final: 0.4778 (m-70) REVERT: A 350 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.5067 (mtt180) REVERT: A 391 CYS cc_start: 0.1724 (OUTLIER) cc_final: -0.0584 (p) REVERT: B 542 MET cc_start: 0.4999 (mmt) cc_final: 0.4728 (mmp) REVERT: C 74 LYS cc_start: 0.7505 (pttt) cc_final: 0.6697 (tptp) REVERT: C 109 HIS cc_start: 0.2373 (OUTLIER) cc_final: 0.0913 (m170) REVERT: D 245 CYS cc_start: 0.1717 (OUTLIER) cc_final: 0.0025 (p) REVERT: D 385 ARG cc_start: 0.3043 (mmm160) cc_final: 0.1657 (mpt180) REVERT: D 425 ARG cc_start: 0.3410 (ptm-80) cc_final: 0.1841 (ptt-90) REVERT: D 440 MET cc_start: 0.2157 (tmm) cc_final: 0.1543 (tmm) REVERT: D 509 ARG cc_start: 0.2225 (mmp-170) cc_final: 0.1159 (mmt180) REVERT: E 542 MET cc_start: 0.6795 (mmm) cc_final: 0.6150 (mmt) REVERT: F 36 ILE cc_start: -0.2581 (mt) cc_final: -0.2942 (mt) REVERT: F 172 PHE cc_start: -0.0514 (m-80) cc_final: -0.1173 (m-80) REVERT: G 125 CYS cc_start: 0.0562 (OUTLIER) cc_final: -0.0031 (p) REVERT: G 265 LEU cc_start: 0.8651 (mt) cc_final: 0.8436 (mp) REVERT: G 377 ILE cc_start: 0.5568 (mp) cc_final: 0.5166 (mm) REVERT: G 391 CYS cc_start: -0.0154 (OUTLIER) cc_final: -0.0681 (p) REVERT: G 438 ARG cc_start: 0.2929 (OUTLIER) cc_final: 0.2244 (mmm160) REVERT: I 94 GLU cc_start: 0.0877 (OUTLIER) cc_final: 0.0436 (tt0) outliers start: 91 outliers final: 69 residues processed: 226 average time/residue: 0.2989 time to fit residues: 100.4832 Evaluate side-chains 222 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 143 time to evaluate : 1.857 ------------------------------------------------------------------------------- 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 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 204 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 290 ILE 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 391 CYS Chi-restraints excluded: chain A residue 400 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 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 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 39 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 VAL 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 C residue 132 CYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 586 ARG 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 131 GLN Chi-restraints excluded: chain F residue 162 THR 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 133 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 280 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 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 GLU 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 94 GLU Chi-restraints excluded: chain I residue 119 THR 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 116 optimal weight: 0.1980 chunk 142 optimal weight: 0.0980 chunk 147 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 170 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 ASN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5322 r_free = 0.5322 target = 0.211912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.179550 restraints weight = 45935.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.176798 restraints weight = 40311.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.178081 restraints weight = 32746.710| |-----------------------------------------------------------------------------| r_work (final): 0.4862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4961 moved from start: 0.8236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16997 Z= 0.146 Angle : 0.833 18.753 23098 Z= 0.405 Chirality : 0.049 0.482 2703 Planarity : 0.005 0.062 2889 Dihedral : 8.536 90.503 2588 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.60 % Favored : 87.35 % Rotamer: Outliers : 4.27 % Allowed : 33.76 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.25 % 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: -3.19 (0.17), residues: 2040 helix: -0.09 (0.27), residues: 327 sheet: -2.07 (0.24), residues: 414 loop : -2.85 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 603 HIS 0.008 0.001 HIS A 293 PHE 0.022 0.002 PHE G 59 TYR 0.026 0.002 TYR A 223 ARG 0.007 0.001 ARG G 462 Details of bonding type rmsd link_NAG-ASN : bond 0.01020 ( 18) link_NAG-ASN : angle 4.76746 ( 54) hydrogen bonds : bond 0.03871 ( 405) hydrogen bonds : angle 5.81952 ( 1017) SS BOND : bond 0.00445 ( 35) SS BOND : angle 1.66468 ( 70) covalent geometry : bond 0.00324 (16944) covalent geometry : angle 0.79713 (22974) ********************** 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 225 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 145 time to evaluate : 1.980 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: A 108 ASN cc_start: 0.5467 (m-40) cc_final: 0.5175 (m-40) REVERT: A 123 LYS cc_start: 0.4354 (OUTLIER) cc_final: 0.2202 (mtmm) REVERT: A 304 ARG cc_start: 0.6463 (mtm-85) cc_final: 0.6196 (mpp-170) REVERT: A 345 HIS cc_start: 0.5190 (OUTLIER) cc_final: 0.4847 (m-70) REVERT: A 350 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.4986 (mtt180) REVERT: A 391 CYS cc_start: 0.1728 (OUTLIER) cc_final: -0.0582 (p) REVERT: B 542 MET cc_start: 0.5301 (mmt) cc_final: 0.5039 (mmp) REVERT: C 74 LYS cc_start: 0.7506 (pttt) cc_final: 0.6899 (mttm) REVERT: C 109 HIS cc_start: 0.2555 (OUTLIER) cc_final: 0.1058 (m170) REVERT: D 245 CYS cc_start: 0.1520 (OUTLIER) cc_final: 0.0031 (p) REVERT: D 385 ARG cc_start: 0.2984 (mmm160) cc_final: 0.1630 (mpt180) REVERT: D 425 ARG cc_start: 0.3387 (ptm-80) cc_final: 0.1801 (ptt-90) REVERT: D 440 MET cc_start: 0.2219 (tmm) cc_final: 0.1578 (tmm) REVERT: D 509 ARG cc_start: 0.2219 (mmp-170) cc_final: 0.1283 (mmt180) REVERT: E 542 MET cc_start: 0.6567 (mmm) cc_final: 0.5980 (mmt) REVERT: E 636 MET cc_start: 0.4989 (ttt) cc_final: 0.4597 (ttt) REVERT: F 36 ILE cc_start: -0.2419 (mt) cc_final: -0.2778 (mt) REVERT: F 172 PHE cc_start: -0.0621 (m-80) cc_final: -0.1205 (m-80) REVERT: G 125 CYS cc_start: 0.0804 (OUTLIER) cc_final: 0.0171 (p) REVERT: G 377 ILE cc_start: 0.5518 (mp) cc_final: 0.5066 (mm) REVERT: G 391 CYS cc_start: 0.0275 (OUTLIER) cc_final: -0.0180 (p) REVERT: G 438 ARG cc_start: 0.2900 (OUTLIER) cc_final: 0.2252 (mmm160) REVERT: H 578 TRP cc_start: 0.6243 (t60) cc_final: 0.6008 (t60) REVERT: I 94 GLU cc_start: 0.1037 (OUTLIER) cc_final: 0.0549 (tt0) outliers start: 80 outliers final: 64 residues processed: 212 average time/residue: 0.3004 time to fit residues: 96.4133 Evaluate side-chains 213 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 139 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 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 204 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 279 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 391 CYS Chi-restraints excluded: chain A residue 400 THR 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 496 GLU Chi-restraints excluded: chain B residue 525 VAL 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 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 88 VAL 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 C residue 132 CYS Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 586 ARG 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 131 GLN 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 136 GLU Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 280 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 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 496 GLU 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 94 GLU 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 119 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 155 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5303 r_free = 0.5303 target = 0.210270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.176274 restraints weight = 45532.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.173682 restraints weight = 41499.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.175226 restraints weight = 32708.640| |-----------------------------------------------------------------------------| r_work (final): 0.4814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5058 moved from start: 0.8424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16997 Z= 0.171 Angle : 0.867 18.170 23098 Z= 0.422 Chirality : 0.050 0.458 2703 Planarity : 0.005 0.062 2889 Dihedral : 8.473 85.252 2588 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.68 % Favored : 86.27 % Rotamer: Outliers : 4.11 % Allowed : 34.13 % Favored : 61.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.20 % 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: -3.13 (0.17), residues: 2040 helix: -0.03 (0.28), residues: 327 sheet: -2.03 (0.25), residues: 378 loop : -2.81 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 603 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 0.006 0.001 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.01032 ( 18) link_NAG-ASN : angle 4.70253 ( 54) hydrogen bonds : bond 0.04130 ( 405) hydrogen bonds : angle 5.93118 ( 1017) SS BOND : bond 0.00463 ( 35) SS BOND : angle 1.59583 ( 70) covalent geometry : bond 0.00388 (16944) covalent geometry : angle 0.83439 (22974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9379.06 seconds wall clock time: 166 minutes 42.93 seconds (10002.93 seconds total)