Starting phenix.real_space_refine on Sun May 18 06:48:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7n_39820/05_2025/8z7n_39820.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7n_39820/05_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_39820/05_2025/8z7n_39820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7n_39820/05_2025/8z7n_39820.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7n_39820/05_2025/8z7n_39820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7n_39820/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.94, 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: 3.80 Conformation dependent library (CDL) restraints added in 1.9 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: 1.80 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: 4.28 Time building geometry restraints manager: 4.49 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: 0.12 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: 5.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 37.180 Find NCS groups from input model: 0.510 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.280 ------------------------------------------------------------------------------- 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 : 1.750 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: 0.2566 time to fit residues: 292.5081 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 : 1.972 ------------------------------------------------------------------------------- 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 = 46259.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.196033 restraints weight = 61631.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5109 r_free = 0.5109 target = 0.196582 restraints weight = 35274.206| |-----------------------------------------------------------------------------| 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 14.809 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 5.25821 ( 54) hydrogen bonds : bond 0.05590 ( 405) hydrogen bonds : angle 7.16995 ( 1017) SS BOND : bond 0.00794 ( 35) SS BOND : angle 2.03276 ( 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 : 1.754 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: 0.6129 (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: 0.0047 (p) REVERT: A 429 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7611 (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: -0.3239 (tpt90) REVERT: D 425 ARG cc_start: 0.3682 (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: 0.4977 (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: 0.1028 (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: 0.0932 (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: 0.2787 time to fit residues: 162.0686 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 : 1.743 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 21 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 174 optimal weight: 0.0770 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN 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 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 167 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.211691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.183009 restraints weight = 45893.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.181328 restraints weight = 41484.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.182470 restraints weight = 35499.165| |-----------------------------------------------------------------------------| r_work (final): 0.4933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4709 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16997 Z= 0.194 Angle : 0.936 14.527 23098 Z= 0.462 Chirality : 0.052 0.404 2703 Planarity : 0.006 0.067 2889 Dihedral : 10.972 110.412 2675 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.17 % Favored : 85.69 % Rotamer: Outliers : 7.59 % Allowed : 28.15 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.23 (0.16), residues: 2040 helix: -0.84 (0.26), residues: 324 sheet: -3.12 (0.21), residues: 396 loop : -3.44 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 159 HIS 0.017 0.002 HIS A 336 PHE 0.028 0.002 PHE G 59 TYR 0.035 0.002 TYR A 223 ARG 0.008 0.001 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.01076 ( 18) link_NAG-ASN : angle 5.12545 ( 54) hydrogen bonds : bond 0.05315 ( 405) hydrogen bonds : angle 6.71791 ( 1017) SS BOND : bond 0.00635 ( 35) SS BOND : angle 1.98379 ( 70) covalent geometry : bond 0.00430 (16944) covalent geometry : angle 0.89791 (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 322 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 180 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6077 (pt) REVERT: A 455 ILE cc_start: 0.5676 (OUTLIER) cc_final: 0.5269 (mm) REVERT: B 537 MET cc_start: 0.5864 (mtt) cc_final: 0.4991 (ttp) REVERT: B 615 VAL cc_start: -0.1419 (OUTLIER) cc_final: -0.2244 (m) REVERT: C 145 THR cc_start: 0.6928 (OUTLIER) cc_final: 0.6373 (p) REVERT: D 199 LEU cc_start: 0.6761 (pt) cc_final: 0.6557 (mp) REVERT: D 245 CYS cc_start: 0.1211 (OUTLIER) cc_final: -0.0013 (p) REVERT: D 509 ARG cc_start: 0.0829 (OUTLIER) cc_final: -0.0053 (mmt180) REVERT: F 26 ILE cc_start: -0.1257 (OUTLIER) cc_final: -0.1869 (mm) REVERT: G 78 HIS cc_start: 0.5961 (t70) cc_final: 0.5649 (t70) REVERT: G 106 MET cc_start: 0.6779 (ttp) cc_final: 0.6560 (ttp) REVERT: G 266 LEU cc_start: 0.4900 (OUTLIER) cc_final: 0.4536 (tp) REVERT: G 391 CYS cc_start: -0.0344 (OUTLIER) cc_final: -0.1573 (p) REVERT: G 424 CYS cc_start: 0.2155 (OUTLIER) cc_final: 0.0330 (t) REVERT: I 5 VAL cc_start: 0.5174 (t) cc_final: 0.4740 (m) REVERT: I 94 GLU cc_start: 0.1354 (OUTLIER) cc_final: 0.0871 (tt0) outliers start: 142 outliers final: 76 residues processed: 302 average time/residue: 0.2593 time to fit residues: 122.1856 Evaluate side-chains 227 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 140 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 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 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 436 VAL Chi-restraints excluded: chain A residue 455 ILE 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 527 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain 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 245 CYS 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 313 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 407 TYR Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 578 TRP Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain 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 266 LEU 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 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 178 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 28 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 HIS ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 336 HIS ** G 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5297 r_free = 0.5297 target = 0.211607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.181918 restraints weight = 45825.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.180949 restraints weight = 40722.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.181824 restraints weight = 33760.389| |-----------------------------------------------------------------------------| r_work (final): 0.4909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4728 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16997 Z= 0.182 Angle : 0.877 13.065 23098 Z= 0.435 Chirality : 0.051 0.403 2703 Planarity : 0.005 0.065 2889 Dihedral : 9.733 108.457 2618 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.38 % Favored : 86.52 % Rotamer: Outliers : 7.00 % Allowed : 29.11 % Favored : 63.89 % 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: -3.91 (0.17), residues: 2040 helix: -0.54 (0.26), residues: 327 sheet: -2.97 (0.22), residues: 390 loop : -3.21 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 603 HIS 0.010 0.001 HIS A 380 PHE 0.024 0.002 PHE G 59 TYR 0.033 0.002 TYR A 223 ARG 0.008 0.001 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.00814 ( 18) link_NAG-ASN : angle 4.03510 ( 54) hydrogen bonds : bond 0.04924 ( 405) hydrogen bonds : angle 6.48754 ( 1017) SS BOND : bond 0.00603 ( 35) SS BOND : angle 1.87181 ( 70) covalent geometry : bond 0.00406 (16944) covalent geometry : angle 0.85079 (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: 131 poor density : 161 time to evaluate : 1.722 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: A 90 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5857 (pt) REVERT: A 108 ASN cc_start: 0.5371 (m-40) cc_final: 0.5142 (m-40) REVERT: A 482 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7022 (mtp85) REVERT: B 537 MET cc_start: 0.5751 (mtt) cc_final: 0.4338 (ttp) REVERT: B 630 TRP cc_start: 0.6025 (m100) cc_final: 0.5227 (m100) REVERT: D 245 CYS cc_start: 0.1247 (OUTLIER) cc_final: -0.0081 (p) REVERT: D 385 ARG cc_start: 0.3249 (mmm160) cc_final: 0.1124 (mmt-90) REVERT: D 440 MET cc_start: 0.2314 (tmm) cc_final: 0.1969 (ppp) REVERT: F 26 ILE cc_start: -0.1034 (OUTLIER) cc_final: -0.1544 (mm) REVERT: G 122 LEU cc_start: 0.5848 (mt) cc_final: 0.5382 (mm) REVERT: G 266 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.4778 (tp) REVERT: G 391 CYS cc_start: -0.0541 (OUTLIER) cc_final: -0.1646 (p) REVERT: G 424 CYS cc_start: 0.1962 (OUTLIER) cc_final: 0.0207 (t) REVERT: H 638 TRP cc_start: 0.7157 (OUTLIER) cc_final: 0.6863 (t-100) REVERT: I 5 VAL cc_start: 0.5372 (t) cc_final: 0.4910 (m) REVERT: I 94 GLU cc_start: 0.1293 (OUTLIER) cc_final: 0.0984 (tt0) REVERT: I 121 GLU cc_start: 0.3825 (OUTLIER) cc_final: 0.3479 (pm20) outliers start: 131 outliers final: 84 residues processed: 275 average time/residue: 0.2575 time to fit residues: 109.6137 Evaluate side-chains 239 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 146 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 242 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 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 406 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 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 634 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 52 LYS 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 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 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 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 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 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 H residue 638 TRP 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 155 ASP Chi-restraints excluded: chain I residue 158 THR Chi-restraints excluded: chain I residue 178 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 157 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 5 optimal weight: 0.0670 chunk 142 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** 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** ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 88 GLN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN D 484 ASN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN F 131 GLN G 358 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5256 r_free = 0.5256 target = 0.214379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.174934 restraints weight = 45627.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.177226 restraints weight = 31482.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.176926 restraints weight = 23149.964| |-----------------------------------------------------------------------------| r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 16997 Z= 0.269 Angle : 0.989 13.690 23098 Z= 0.500 Chirality : 0.055 0.484 2703 Planarity : 0.006 0.076 2889 Dihedral : 10.047 101.252 2609 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.42 % Favored : 83.53 % Rotamer: Outliers : 7.80 % Allowed : 29.86 % Favored : 62.34 % 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: -4.14 (0.16), residues: 2040 helix: -1.20 (0.24), residues: 366 sheet: -2.99 (0.22), residues: 411 loop : -3.32 (0.15), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 603 HIS 0.011 0.002 HIS A 255 PHE 0.024 0.003 PHE G 59 TYR 0.053 0.003 TYR A 223 ARG 0.015 0.001 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.00832 ( 18) link_NAG-ASN : angle 4.20369 ( 54) hydrogen bonds : bond 0.05854 ( 405) hydrogen bonds : angle 6.79832 ( 1017) SS BOND : bond 0.00984 ( 35) SS BOND : angle 2.39234 ( 70) covalent geometry : bond 0.00611 (16944) covalent geometry : angle 0.96159 (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 307 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 161 time to evaluate : 1.837 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: 0.6811 (OUTLIER) cc_final: 0.6445 (pt) REVERT: A 108 ASN cc_start: 0.5580 (m-40) cc_final: 0.5234 (m-40) REVERT: A 123 LYS cc_start: 0.4849 (OUTLIER) cc_final: 0.2797 (mtmm) REVERT: A 453 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7778 (p) REVERT: A 483 ASP cc_start: 0.6712 (OUTLIER) cc_final: 0.6177 (m-30) REVERT: B 537 MET cc_start: 0.5892 (mtt) cc_final: 0.4544 (mtt) REVERT: C 109 HIS cc_start: 0.2237 (OUTLIER) cc_final: 0.0795 (m170) REVERT: D 304 ARG cc_start: 0.2824 (ptp90) cc_final: 0.0582 (tmt170) REVERT: D 314 ARG cc_start: -0.1374 (OUTLIER) cc_final: -0.2687 (tpt90) REVERT: D 385 ARG cc_start: 0.3158 (mmm160) cc_final: 0.1349 (mpt180) REVERT: D 402 MET cc_start: 0.0651 (mmm) cc_final: 0.0300 (mmm) REVERT: D 425 ARG cc_start: 0.3439 (ptm-80) cc_final: 0.1970 (ptt-90) REVERT: D 445 ILE cc_start: 0.1635 (OUTLIER) cc_final: 0.1337 (mp) REVERT: D 509 ARG cc_start: 0.1283 (OUTLIER) cc_final: 0.0449 (mmt180) REVERT: F 36 ILE cc_start: -0.2621 (mt) cc_final: -0.3338 (mm) REVERT: F 172 PHE cc_start: -0.1276 (m-80) cc_final: -0.2164 (m-80) REVERT: G 52 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.5941 (tptp) REVERT: G 125 CYS cc_start: 0.0317 (OUTLIER) cc_final: -0.0256 (p) REVERT: G 266 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5296 (tp) REVERT: G 391 CYS cc_start: -0.0108 (OUTLIER) cc_final: -0.1065 (p) REVERT: G 424 CYS cc_start: 0.0667 (OUTLIER) cc_final: -0.1177 (t) REVERT: G 438 ARG cc_start: 0.2778 (OUTLIER) cc_final: 0.2161 (mmm160) REVERT: H 638 TRP cc_start: 0.7555 (OUTLIER) cc_final: 0.7050 (t-100) REVERT: I 94 GLU cc_start: 0.0453 (OUTLIER) cc_final: 0.0179 (tt0) REVERT: I 121 GLU cc_start: 0.3953 (OUTLIER) cc_final: 0.3435 (pm20) REVERT: I 140 ILE cc_start: 0.1597 (OUTLIER) cc_final: 0.1295 (tp) outliers start: 146 outliers final: 90 residues processed: 286 average time/residue: 0.2921 time to fit residues: 123.6349 Evaluate side-chains 251 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 143 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 242 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 301 VAL 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 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 527 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 612 CYS 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 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 D residue 45 TYR Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 80 CYS Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 309 THR 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 445 ILE Chi-restraints excluded: chain D residue 491 LYS Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 509 ARG Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 585 THR 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 596 ASP Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 52 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 225 THR Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 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 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 473 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 H residue 632 ASN Chi-restraints excluded: chain H residue 638 TRP 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 178 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 198 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 111 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 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 GLN B 626 GLN ** 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** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 484 ASN ** 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 = 0.5240 r_free = 0.5240 target = 0.205666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.169460 restraints weight = 46017.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.166342 restraints weight = 43138.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.167838 restraints weight = 33957.408| |-----------------------------------------------------------------------------| r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16997 Z= 0.269 Angle : 0.970 14.754 23098 Z= 0.490 Chirality : 0.054 0.452 2703 Planarity : 0.006 0.075 2889 Dihedral : 10.019 100.497 2605 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 27.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.15 % Favored : 84.80 % Rotamer: Outliers : 7.91 % Allowed : 30.18 % Favored : 61.91 % 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: -4.03 (0.16), residues: 2040 helix: -1.09 (0.25), residues: 339 sheet: -2.72 (0.24), residues: 342 loop : -3.32 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 41 HIS 0.013 0.002 HIS A 255 PHE 0.022 0.003 PHE G 59 TYR 0.058 0.003 TYR A 223 ARG 0.015 0.001 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.01002 ( 18) link_NAG-ASN : angle 3.76629 ( 54) hydrogen bonds : bond 0.05740 ( 405) hydrogen bonds : angle 6.78298 ( 1017) SS BOND : bond 0.00772 ( 35) SS BOND : angle 2.11922 ( 70) covalent geometry : bond 0.00618 (16944) covalent geometry : angle 0.94859 (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 297 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 149 time to evaluate : 1.706 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: 0.6834 (OUTLIER) cc_final: 0.6516 (pt) REVERT: A 108 ASN cc_start: 0.5471 (m-40) cc_final: 0.5145 (m-40) REVERT: A 123 LYS cc_start: 0.4820 (OUTLIER) cc_final: 0.2883 (mtmm) REVERT: A 310 ARG cc_start: 0.5984 (mpt180) cc_final: 0.5110 (tpm170) REVERT: A 440 MET cc_start: 0.6210 (mmt) cc_final: 0.5802 (mmp) REVERT: B 537 MET cc_start: 0.5694 (mtt) cc_final: 0.4422 (mtt) REVERT: B 593 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6964 (t80) REVERT: C 109 HIS cc_start: 0.2290 (OUTLIER) cc_final: 0.0750 (m170) REVERT: D 252 GLN cc_start: 0.6515 (tt0) cc_final: 0.6306 (tp40) REVERT: D 291 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6991 (tt) REVERT: D 314 ARG cc_start: -0.1037 (OUTLIER) cc_final: -0.2567 (tpt90) REVERT: D 385 ARG cc_start: 0.3095 (mmm160) cc_final: 0.1487 (mpt180) REVERT: D 425 ARG cc_start: 0.3706 (ptm-80) cc_final: 0.2057 (ptt-90) REVERT: F 36 ILE cc_start: -0.2751 (mt) cc_final: -0.3157 (mt) REVERT: F 172 PHE cc_start: -0.1283 (m-80) cc_final: -0.2087 (m-80) REVERT: G 265 LEU cc_start: 0.8706 (mt) cc_final: 0.8453 (mp) REVERT: G 266 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.4632 (tp) REVERT: G 391 CYS cc_start: -0.0365 (OUTLIER) cc_final: -0.1008 (p) REVERT: G 438 ARG cc_start: 0.3206 (OUTLIER) cc_final: 0.2416 (mmm160) REVERT: H 638 TRP cc_start: 0.7265 (OUTLIER) cc_final: 0.6738 (t-100) REVERT: I 94 GLU cc_start: 0.0669 (OUTLIER) cc_final: 0.0314 (tt0) REVERT: I 121 GLU cc_start: 0.4009 (OUTLIER) cc_final: 0.3533 (pm20) outliers start: 148 outliers final: 104 residues processed: 281 average time/residue: 0.2896 time to fit residues: 121.4041 Evaluate side-chains 255 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 139 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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 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 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 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 527 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 593 TYR 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 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 132 CYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 80 CYS Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 291 LEU 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 314 ARG Chi-restraints excluded: chain D residue 351 VAL 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 482 ARG Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 131 GLN 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 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 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 338 ASN Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ARG Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 629 ILE Chi-restraints excluded: chain H residue 632 ASN Chi-restraints excluded: chain H residue 638 TRP 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=2.50 ------------------------------------------------------------------------------- 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: 6.9990 chunk 120 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 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 547 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** ** 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** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5272 r_free = 0.5272 target = 0.208614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.179249 restraints weight = 45862.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.179116 restraints weight = 51780.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.179894 restraints weight = 38180.004| |-----------------------------------------------------------------------------| r_work (final): 0.4909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4773 moved from start: 0.7508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16997 Z= 0.181 Angle : 0.882 14.797 23098 Z= 0.435 Chirality : 0.050 0.447 2703 Planarity : 0.005 0.059 2889 Dihedral : 9.584 97.842 2602 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.26 % Favored : 85.69 % Rotamer: Outliers : 6.57 % Allowed : 32.05 % Favored : 61.38 % 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: -3.72 (0.17), residues: 2040 helix: -0.52 (0.27), residues: 333 sheet: -2.66 (0.24), residues: 363 loop : -3.13 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 41 HIS 0.010 0.001 HIS A 255 PHE 0.022 0.002 PHE G 59 TYR 0.038 0.002 TYR A 223 ARG 0.008 0.001 ARG A 385 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 18) link_NAG-ASN : angle 4.56163 ( 54) hydrogen bonds : bond 0.04700 ( 405) hydrogen bonds : angle 6.33510 ( 1017) SS BOND : bond 0.00564 ( 35) SS BOND : angle 1.79738 ( 70) covalent geometry : bond 0.00406 (16944) covalent geometry : angle 0.85066 (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 284 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 161 time to evaluate : 1.761 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: 0.6717 (OUTLIER) cc_final: 0.6448 (pt) REVERT: A 108 ASN cc_start: 0.5577 (m-40) cc_final: 0.5267 (m-40) REVERT: A 123 LYS cc_start: 0.4560 (OUTLIER) cc_final: 0.2770 (mtmm) REVERT: A 350 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.5207 (mtt180) REVERT: B 537 MET cc_start: 0.5658 (mtt) cc_final: 0.4331 (mtt) REVERT: C 74 LYS cc_start: 0.7464 (pttt) cc_final: 0.6679 (tptt) REVERT: C 109 HIS cc_start: 0.2158 (OUTLIER) cc_final: 0.0638 (m170) REVERT: C 145 THR cc_start: 0.7166 (m) cc_final: 0.6579 (p) REVERT: D 385 ARG cc_start: 0.3141 (mmm160) cc_final: 0.1567 (mpt180) REVERT: D 425 ARG cc_start: 0.3889 (ptm-80) cc_final: 0.2151 (ptt-90) REVERT: D 440 MET cc_start: 0.2260 (tmm) cc_final: 0.1800 (tmm) REVERT: E 542 MET cc_start: 0.6645 (mmm) cc_final: 0.5882 (mmt) REVERT: F 36 ILE cc_start: -0.2120 (mt) cc_final: -0.2511 (mt) REVERT: G 125 CYS cc_start: 0.1266 (OUTLIER) cc_final: 0.0427 (p) REVERT: G 266 LEU cc_start: 0.4949 (OUTLIER) cc_final: 0.4121 (tp) REVERT: G 377 ILE cc_start: 0.5003 (mp) cc_final: 0.4740 (mm) REVERT: G 391 CYS cc_start: -0.0268 (OUTLIER) cc_final: -0.0861 (p) REVERT: G 438 ARG cc_start: 0.3315 (OUTLIER) cc_final: 0.2487 (mmm160) REVERT: H 638 TRP cc_start: 0.7018 (OUTLIER) cc_final: 0.6803 (t-100) REVERT: I 94 GLU cc_start: 0.1424 (OUTLIER) cc_final: 0.1005 (tt0) REVERT: I 121 GLU cc_start: 0.3741 (OUTLIER) cc_final: 0.3535 (pm20) outliers start: 123 outliers final: 87 residues processed: 268 average time/residue: 0.2765 time to fit residues: 110.9170 Evaluate side-chains 239 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 141 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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 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 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 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 590 ILE 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 38 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 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 45 TYR Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 111 HIS 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 400 THR Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain 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 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 396 LEU Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ARG Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain H residue 545 THR Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 632 ASN Chi-restraints excluded: chain H residue 638 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 187 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 172 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 85 optimal weight: 0.0870 chunk 174 optimal weight: 2.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- 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 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** B 547 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 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN F 165 GLN G 285 ASN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 584 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.209388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.178006 restraints weight = 45745.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.177077 restraints weight = 40132.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.178209 restraints weight = 31617.136| |-----------------------------------------------------------------------------| r_work (final): 0.4866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4856 moved from start: 0.7781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16997 Z= 0.172 Angle : 0.858 14.391 23098 Z= 0.424 Chirality : 0.049 0.421 2703 Planarity : 0.005 0.061 2889 Dihedral : 9.239 95.599 2597 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.02 % Favored : 85.93 % Rotamer: Outliers : 6.57 % Allowed : 32.05 % Favored : 61.38 % 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: -3.49 (0.17), residues: 2040 helix: -0.24 (0.27), residues: 324 sheet: -2.34 (0.24), residues: 372 loop : -3.04 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B 603 HIS 0.010 0.001 HIS A 255 PHE 0.022 0.002 PHE G 59 TYR 0.036 0.002 TYR A 223 ARG 0.006 0.001 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.00850 ( 18) link_NAG-ASN : angle 4.15739 ( 54) hydrogen bonds : bond 0.04438 ( 405) hydrogen bonds : angle 6.19476 ( 1017) SS BOND : bond 0.00535 ( 35) SS BOND : angle 1.66598 ( 70) covalent geometry : bond 0.00383 (16944) covalent geometry : angle 0.83138 (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 268 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 145 time to evaluate : 1.899 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: A 90 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6501 (pt) REVERT: A 108 ASN cc_start: 0.5518 (m-40) cc_final: 0.5163 (m-40) REVERT: A 123 LYS cc_start: 0.4464 (OUTLIER) cc_final: 0.2516 (mtmm) REVERT: A 345 HIS cc_start: 0.5262 (OUTLIER) cc_final: 0.4570 (m-70) REVERT: A 350 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.4959 (mtt180) REVERT: A 377 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.6973 (tp) REVERT: A 391 CYS cc_start: 0.1819 (OUTLIER) cc_final: -0.0538 (p) REVERT: A 440 MET cc_start: 0.6598 (mmp) cc_final: 0.6177 (mmp) REVERT: B 537 MET cc_start: 0.5516 (mtt) cc_final: 0.4170 (mtt) REVERT: C 109 HIS cc_start: 0.2390 (OUTLIER) cc_final: 0.0820 (m170) REVERT: C 145 THR cc_start: 0.7181 (m) cc_final: 0.6592 (p) REVERT: D 314 ARG cc_start: -0.1049 (OUTLIER) cc_final: -0.2706 (tpt90) REVERT: D 440 MET cc_start: 0.2604 (tmm) cc_final: 0.2296 (tmm) REVERT: E 542 MET cc_start: 0.6626 (mmm) cc_final: 0.5946 (mmt) REVERT: F 36 ILE cc_start: -0.2046 (mt) cc_final: -0.2456 (mt) REVERT: G 125 CYS cc_start: 0.1118 (OUTLIER) cc_final: 0.0348 (p) REVERT: G 377 ILE cc_start: 0.5128 (mp) cc_final: 0.4885 (mm) REVERT: G 391 CYS cc_start: -0.0322 (OUTLIER) cc_final: -0.0899 (p) REVERT: G 438 ARG cc_start: 0.3271 (OUTLIER) cc_final: 0.2553 (mmm160) REVERT: H 638 TRP cc_start: 0.6883 (OUTLIER) cc_final: 0.6648 (t-100) REVERT: I 94 GLU cc_start: 0.1184 (OUTLIER) cc_final: 0.0742 (tt0) outliers start: 123 outliers final: 82 residues processed: 251 average time/residue: 0.2691 time to fit residues: 103.0121 Evaluate side-chains 225 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 130 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 271 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE 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 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 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 38 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 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 45 TYR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 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 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 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 371 SER Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain H residue 638 TRP 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: 7.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 102 optimal weight: 0.0170 chunk 39 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- 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 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** ** E 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 ASN ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 139 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.210364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.179828 restraints weight = 45845.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.180074 restraints weight = 39092.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.180501 restraints weight = 30186.096| |-----------------------------------------------------------------------------| r_work (final): 0.4904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4762 moved from start: 0.8071 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= 0.155 Angle : 0.859 20.674 23098 Z= 0.417 Chirality : 0.050 0.482 2703 Planarity : 0.005 0.064 2889 Dihedral : 8.922 92.289 2592 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.87 % Favored : 86.08 % Rotamer: Outliers : 5.29 % Allowed : 32.80 % Favored : 61.91 % 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: -3.35 (0.17), residues: 2040 helix: -0.24 (0.27), residues: 333 sheet: -2.32 (0.24), residues: 393 loop : -2.90 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 603 HIS 0.009 0.001 HIS A 255 PHE 0.022 0.002 PHE G 59 TYR 0.029 0.002 TYR A 223 ARG 0.011 0.001 ARG G 462 Details of bonding type rmsd link_NAG-ASN : bond 0.01056 ( 18) link_NAG-ASN : angle 4.92188 ( 54) hydrogen bonds : bond 0.04072 ( 405) hydrogen bonds : angle 6.03885 ( 1017) SS BOND : bond 0.00473 ( 35) SS BOND : angle 1.67040 ( 70) covalent geometry : bond 0.00346 (16944) covalent geometry : angle 0.82260 (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 240 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 141 time to evaluate : 1.797 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: 0.5548 (m-40) cc_final: 0.5173 (m-40) REVERT: A 123 LYS cc_start: 0.4294 (OUTLIER) cc_final: 0.2345 (mtmm) REVERT: A 345 HIS cc_start: 0.5115 (OUTLIER) cc_final: 0.4561 (m-70) REVERT: A 350 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.5057 (mtt180) REVERT: A 377 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.6884 (tp) REVERT: A 391 CYS cc_start: 0.1625 (OUTLIER) cc_final: -0.0695 (p) REVERT: A 440 MET cc_start: 0.6553 (mmp) cc_final: 0.6156 (mmp) REVERT: B 542 MET cc_start: 0.5134 (mmt) cc_final: 0.4801 (mmp) REVERT: C 74 LYS cc_start: 0.7462 (pttt) cc_final: 0.6612 (tptt) REVERT: C 109 HIS cc_start: 0.2396 (OUTLIER) cc_final: 0.0918 (m170) REVERT: C 145 THR cc_start: 0.7146 (m) cc_final: 0.6564 (p) REVERT: E 542 MET cc_start: 0.6546 (mmm) cc_final: 0.5920 (mmt) REVERT: F 36 ILE cc_start: -0.2168 (mt) cc_final: -0.2577 (mt) REVERT: G 125 CYS cc_start: 0.1191 (OUTLIER) cc_final: 0.0407 (p) REVERT: G 377 ILE cc_start: 0.5201 (mp) cc_final: 0.4950 (mm) REVERT: G 391 CYS cc_start: 0.0366 (OUTLIER) cc_final: -0.0080 (p) REVERT: G 438 ARG cc_start: 0.3181 (OUTLIER) cc_final: 0.2413 (mmm160) REVERT: H 638 TRP cc_start: 0.7049 (OUTLIER) cc_final: 0.6664 (t-100) REVERT: I 94 GLU cc_start: 0.1343 (OUTLIER) cc_final: 0.0854 (tt0) outliers start: 99 outliers final: 78 residues processed: 228 average time/residue: 0.2684 time to fit residues: 94.1258 Evaluate side-chains 220 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 131 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 245 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE 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 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 586 ARG 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 38 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 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 162 THR Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 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 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 396 LEU Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain H residue 545 THR Chi-restraints excluded: chain H residue 638 TRP 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: 0.0970 chunk 142 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 246 HIS ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** 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** ** E 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 ASN ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5279 r_free = 0.5279 target = 0.209247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.173930 restraints weight = 45681.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.170725 restraints weight = 38062.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.171464 restraints weight = 36365.067| |-----------------------------------------------------------------------------| r_work (final): 0.4764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5236 moved from start: 0.8301 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= 0.172 Angle : 0.872 20.080 23098 Z= 0.424 Chirality : 0.050 0.599 2703 Planarity : 0.005 0.062 2889 Dihedral : 8.764 88.913 2592 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.12 % Favored : 85.88 % Rotamer: Outliers : 5.24 % Allowed : 33.28 % Favored : 61.49 % 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: -3.30 (0.17), residues: 2040 helix: -0.26 (0.27), residues: 339 sheet: -2.29 (0.24), residues: 393 loop : -2.87 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 603 HIS 0.010 0.001 HIS A 255 PHE 0.021 0.002 PHE G 59 TYR 0.039 0.002 TYR A 223 ARG 0.007 0.001 ARG G 462 Details of bonding type rmsd link_NAG-ASN : bond 0.01021 ( 18) link_NAG-ASN : angle 4.92843 ( 54) hydrogen bonds : bond 0.04210 ( 405) hydrogen bonds : angle 6.09179 ( 1017) SS BOND : bond 0.00484 ( 35) SS BOND : angle 1.68782 ( 70) covalent geometry : bond 0.00388 (16944) covalent geometry : angle 0.83548 (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 232 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 134 time to evaluate : 2.055 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: 0.5524 (m-40) cc_final: 0.5126 (m-40) REVERT: A 123 LYS cc_start: 0.4290 (OUTLIER) cc_final: 0.2287 (mtmm) REVERT: A 345 HIS cc_start: 0.5154 (OUTLIER) cc_final: 0.4537 (m-70) REVERT: A 377 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6946 (tp) REVERT: A 440 MET cc_start: 0.6570 (mmp) cc_final: 0.6181 (mmp) REVERT: B 542 MET cc_start: 0.5113 (mmt) cc_final: 0.4787 (mmp) REVERT: C 15 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5833 (tp30) REVERT: C 109 HIS cc_start: 0.2379 (OUTLIER) cc_final: 0.0921 (m170) REVERT: C 145 THR cc_start: 0.7300 (m) cc_final: 0.6711 (p) REVERT: D 104 ASN cc_start: 0.3686 (OUTLIER) cc_final: 0.3081 (p0) REVERT: E 542 MET cc_start: 0.6780 (mmm) cc_final: 0.6207 (mmt) REVERT: F 36 ILE cc_start: -0.2334 (mt) cc_final: -0.2753 (mt) REVERT: G 125 CYS cc_start: 0.0383 (OUTLIER) cc_final: -0.0103 (p) REVERT: G 377 ILE cc_start: 0.5864 (mp) cc_final: 0.5634 (mm) REVERT: G 391 CYS cc_start: 0.0615 (OUTLIER) cc_final: 0.0193 (p) REVERT: G 438 ARG cc_start: 0.3143 (OUTLIER) cc_final: 0.2432 (mmm160) REVERT: H 633 MET cc_start: 0.6790 (ptm) cc_final: 0.6495 (ptm) REVERT: H 638 TRP cc_start: 0.7276 (OUTLIER) cc_final: 0.6782 (t-100) REVERT: I 94 GLU cc_start: 0.0714 (OUTLIER) cc_final: 0.0308 (tt0) outliers start: 98 outliers final: 78 residues processed: 219 average time/residue: 0.2689 time to fit residues: 90.8784 Evaluate side-chains 218 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 129 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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 245 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 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 590 ILE Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain C residue 15 GLU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 496 GLU Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 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 136 GLU Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 313 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 496 GLU Chi-restraints excluded: chain H residue 545 THR Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 638 TRP 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 119 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 35 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 95 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 550 GLN ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5314 r_free = 0.5314 target = 0.212396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.179243 restraints weight = 45915.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.176175 restraints weight = 43663.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.178068 restraints weight = 36052.471| |-----------------------------------------------------------------------------| r_work (final): 0.4845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4910 moved from start: 0.8531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16997 Z= 0.135 Angle : 0.823 18.908 23098 Z= 0.397 Chirality : 0.049 0.525 2703 Planarity : 0.005 0.073 2889 Dihedral : 8.210 83.140 2592 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 4.54 % Allowed : 33.81 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.18 (0.18), residues: 2040 helix: -0.15 (0.26), residues: 354 sheet: -2.18 (0.24), residues: 399 loop : -2.83 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 603 HIS 0.008 0.001 HIS A 293 PHE 0.022 0.001 PHE G 59 TYR 0.017 0.001 TYR A 223 ARG 0.004 0.000 ARG G 462 Details of bonding type rmsd link_NAG-ASN : bond 0.00990 ( 18) link_NAG-ASN : angle 4.68141 ( 54) hydrogen bonds : bond 0.03656 ( 405) hydrogen bonds : angle 5.88449 ( 1017) SS BOND : bond 0.00427 ( 35) SS BOND : angle 1.44167 ( 70) covalent geometry : bond 0.00292 (16944) covalent geometry : angle 0.78945 (22974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8025.02 seconds wall clock time: 141 minutes 29.53 seconds (8489.53 seconds total)