Starting phenix.real_space_refine on Thu Sep 18 12:12:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7n_39820/09_2025/8z7n_39820.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7n_39820/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z7n_39820/09_2025/8z7n_39820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7n_39820/09_2025/8z7n_39820.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z7n_39820/09_2025/8z7n_39820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7n_39820/09_2025/8z7n_39820.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.84, per 1000 atoms: 0.23 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: 1.21 Conformation dependent library (CDL) restraints added in 503.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.54 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: 2.11 Time building geometry restraints manager: 1.58 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.940 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: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.790 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- 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 : 53.31 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.002 ARG G 462 TYR 0.032 0.003 TYR G 223 PHE 0.019 0.004 PHE G 397 TRP 0.043 0.003 TRP H 635 HIS 0.008 0.002 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00987 (16944) covalent geometry : angle 1.35280 (22974) SS BOND : bond 0.03107 ( 35) SS BOND : angle 3.96304 ( 70) hydrogen bonds : bond 0.22744 ( 405) hydrogen bonds : angle 9.25485 ( 1017) link_NAG-ASN : bond 0.01372 ( 18) link_NAG-ASN : angle 4.22051 ( 54) *********************** 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 : 0.695 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: A 63 ASP cc_start: 0.6290 (t0) cc_final: 0.5932 (t0) REVERT: A 67 TYR cc_start: 0.4957 (OUTLIER) cc_final: 0.4604 (t80) REVERT: A 86 SER cc_start: 0.3964 (OUTLIER) cc_final: 0.3589 (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: 0.5032 (tm-30) REVERT: A 137 CYS cc_start: 0.2946 (OUTLIER) cc_final: 0.2007 (t) REVERT: A 266 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6545 (pt) REVERT: A 314 ARG cc_start: 0.0306 (OUTLIER) cc_final: -0.2094 (tpp-160) REVERT: A 341 LYS cc_start: 0.5989 (OUTLIER) cc_final: 0.5570 (mttt) REVERT: A 376 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: A 396 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5434 (tp) REVERT: A 424 CYS cc_start: 0.2083 (OUTLIER) cc_final: 0.0929 (p) REVERT: A 426 ILE cc_start: 0.4801 (OUTLIER) cc_final: 0.4539 (pt) REVERT: A 429 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7878 (mp) REVERT: A 440 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6186 (mmt) REVERT: B 537 MET cc_start: 0.6616 (mtt) cc_final: 0.5424 (ttt) REVERT: B 627 LYS cc_start: 0.6839 (mtmm) cc_final: 0.6484 (ptmm) REVERT: B 646 THR cc_start: 0.4148 (OUTLIER) cc_final: 0.3947 (m) REVERT: B 663 ASN cc_start: 0.3918 (OUTLIER) cc_final: 0.3481 (m-40) REVERT: C 13 THR cc_start: 0.7084 (m) cc_final: 0.6880 (m) REVERT: C 97 LEU cc_start: 0.5374 (OUTLIER) cc_final: 0.5119 (tp) REVERT: C 109 HIS cc_start: 0.1733 (OUTLIER) cc_final: 0.0785 (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: 0.3406 (mm-30) REVERT: D 232 LEU cc_start: 0.1922 (OUTLIER) cc_final: 0.1072 (tp) REVERT: D 303 THR cc_start: 0.2185 (OUTLIER) cc_final: 0.1507 (m) REVERT: D 304 ARG cc_start: 0.2699 (OUTLIER) cc_final: 0.2038 (tpt90) REVERT: D 341 LYS cc_start: 0.0336 (OUTLIER) cc_final: -0.0197 (ptpp) REVERT: D 425 ARG cc_start: 0.3052 (ptm-80) cc_final: 0.1418 (ptt-90) REVERT: D 430 ILE cc_start: -0.1325 (OUTLIER) cc_final: -0.1576 (pt) REVERT: E 542 MET cc_start: 0.7328 (mmt) cc_final: 0.7111 (mmm) REVERT: E 646 THR cc_start: 0.3467 (OUTLIER) cc_final: 0.3131 (m) REVERT: E 664 GLU cc_start: 0.1168 (OUTLIER) cc_final: 0.0571 (mm-30) REVERT: F 26 ILE cc_start: -0.1344 (OUTLIER) cc_final: -0.1914 (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: -0.1797 (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: 0.2900 (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: 0.6044 (tttp) REVERT: G 232 LEU cc_start: 0.2397 (OUTLIER) cc_final: 0.1511 (tp) REVERT: G 266 LEU cc_start: 0.4343 (OUTLIER) cc_final: 0.3730 (tp) REVERT: G 280 SER cc_start: 0.1819 (OUTLIER) cc_final: 0.1363 (t) REVERT: G 288 LYS cc_start: 0.3077 (OUTLIER) cc_final: 0.1824 (mmtm) REVERT: G 294 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6287 (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: 0.0236 (t) REVERT: G 389 PHE cc_start: 0.2763 (m-80) cc_final: 0.2559 (m-10) REVERT: G 424 CYS cc_start: 0.1689 (OUTLIER) cc_final: 0.0825 (m) REVERT: H 537 MET cc_start: 0.1507 (mtt) cc_final: 0.1016 (mtt) REVERT: H 542 MET cc_start: 0.5273 (mmt) cc_final: 0.4879 (mmm) REVERT: H 664 GLU cc_start: 0.4843 (OUTLIER) cc_final: 0.3580 (tp30) REVERT: I 17 THR cc_start: 0.6126 (OUTLIER) cc_final: 0.5799 (p) REVERT: I 34 ASN cc_start: 0.5977 (OUTLIER) cc_final: 0.5422 (p0) REVERT: I 44 SER cc_start: 0.2682 (OUTLIER) cc_final: 0.2361 (p) REVERT: I 47 THR cc_start: 0.0443 (OUTLIER) cc_final: 0.0217 (p) REVERT: I 100 PHE cc_start: 0.4084 (OUTLIER) cc_final: 0.2433 (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: 0.1393 (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: 0.6017 (p) REVERT: I 163 VAL cc_start: 0.5216 (OUTLIER) cc_final: 0.4521 (p) REVERT: I 171 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6202 (tp30) REVERT: I 172 PHE cc_start: 0.7063 (m-80) cc_final: 0.6736 (t80) outliers start: 555 outliers final: 126 residues processed: 754 average time/residue: 0.1307 time to fit residues: 151.0371 Evaluate side-chains 357 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 177 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 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 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 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 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 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 0.0370 chunk 122 optimal weight: 5.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS A 285 ASN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN A 307 ASN A 454 ASN ** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN 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 D 336 HIS D 484 ASN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 ASN ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 484 ASN ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 658 ASN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN I 41 ASN I 66 GLN I 167 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.210733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.176656 restraints weight = 46040.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.174635 restraints weight = 45943.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.175893 restraints weight = 33884.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.176145 restraints weight = 26951.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.176177 restraints weight = 26571.379| |-----------------------------------------------------------------------------| r_work (final): 0.4832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4954 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 16997 Z= 0.238 Angle : 1.077 15.271 23098 Z= 0.538 Chirality : 0.058 0.503 2703 Planarity : 0.007 0.067 2889 Dihedral : 13.296 103.513 2884 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 27.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.80 % Favored : 85.20 % Rotamer: Outliers : 11.43 % Allowed : 27.30 % Favored : 61.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.96 (0.15), residues: 2040 helix: -1.70 (0.25), residues: 306 sheet: -3.67 (0.20), residues: 402 loop : -3.80 (0.14), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 279 TYR 0.044 0.003 TYR A 223 PHE 0.039 0.003 PHE G 59 TRP 0.028 0.002 TRP C 159 HIS 0.012 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00521 (16944) covalent geometry : angle 1.04351 (22974) SS BOND : bond 0.00885 ( 35) SS BOND : angle 1.99981 ( 70) hydrogen bonds : bond 0.06223 ( 405) hydrogen bonds : angle 7.39604 ( 1017) link_NAG-ASN : bond 0.01418 ( 18) link_NAG-ASN : angle 5.28123 ( 54) *********************** 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 411 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 197 time to evaluate : 0.713 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: A 293 HIS cc_start: 0.5191 (OUTLIER) cc_final: 0.4791 (m170) REVERT: A 314 ARG cc_start: 0.0425 (OUTLIER) cc_final: 0.0206 (pmt-80) REVERT: A 455 ILE cc_start: 0.5659 (OUTLIER) cc_final: 0.5385 (mm) REVERT: A 498 LYS cc_start: 0.7584 (tttt) cc_final: 0.7132 (tptt) REVERT: B 537 MET cc_start: 0.6171 (mtt) cc_final: 0.4931 (ttp) REVERT: B 599 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6655 (mm) REVERT: B 615 VAL cc_start: -0.0579 (OUTLIER) cc_final: -0.1273 (m) REVERT: B 627 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6982 (pttp) REVERT: B 646 THR cc_start: 0.4272 (OUTLIER) cc_final: 0.3905 (m) REVERT: C 145 THR cc_start: 0.7083 (OUTLIER) cc_final: 0.6518 (p) REVERT: D 199 LEU cc_start: 0.6920 (pt) cc_final: 0.6580 (pp) REVERT: D 278 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6892 (tt) REVERT: D 314 ARG cc_start: -0.1851 (OUTLIER) cc_final: -0.3337 (tpt170) REVERT: D 354 LYS cc_start: 0.5478 (OUTLIER) cc_final: 0.5086 (pttp) REVERT: D 425 ARG cc_start: 0.3326 (ptm-80) cc_final: 0.2087 (ptt-90) REVERT: F 26 ILE cc_start: -0.0819 (OUTLIER) cc_final: -0.1079 (mp) REVERT: F 36 ILE cc_start: -0.2405 (OUTLIER) cc_final: -0.2922 (mm) REVERT: G 78 HIS cc_start: 0.6390 (t70) cc_final: 0.5940 (t70) REVERT: G 106 MET cc_start: 0.6811 (ttp) cc_final: 0.6600 (ttp) REVERT: G 136 GLU cc_start: 0.0792 (OUTLIER) cc_final: -0.0071 (tm-30) REVERT: G 266 LEU cc_start: 0.5166 (OUTLIER) cc_final: 0.4444 (tp) REVERT: G 279 ARG cc_start: 0.5510 (OUTLIER) cc_final: 0.4013 (mtm110) REVERT: G 288 LYS cc_start: 0.2863 (OUTLIER) cc_final: 0.1832 (mmtm) REVERT: G 391 CYS cc_start: -0.0379 (OUTLIER) cc_final: -0.1468 (p) REVERT: G 424 CYS cc_start: 0.1854 (OUTLIER) cc_final: -0.0050 (t) REVERT: H 537 MET cc_start: 0.0563 (mtt) cc_final: -0.0770 (mtt) REVERT: H 542 MET cc_start: 0.5150 (mmt) cc_final: 0.4897 (mmm) REVERT: I 94 GLU cc_start: 0.0869 (OUTLIER) cc_final: 0.0508 (tt0) REVERT: I 162 THR cc_start: -0.4272 (OUTLIER) cc_final: -0.4595 (p) REVERT: I 172 PHE cc_start: 0.6748 (m-80) cc_final: 0.6530 (m-80) outliers start: 214 outliers final: 97 residues processed: 390 average time/residue: 0.1305 time to fit residues: 77.4205 Evaluate side-chains 270 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 152 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 118 TRP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 134 THR 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 239 PHE Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 266 LEU 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 293 HIS Chi-restraints excluded: chain A residue 297 SER 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 338 ASN Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 62 SER 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 58 LEU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 407 TYR Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 578 TRP Chi-restraints excluded: chain E residue 593 TYR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 279 ARG 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 301 VAL Chi-restraints excluded: chain G residue 309 THR 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 358 HIS Chi-restraints excluded: chain G residue 365 ASN 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 461 VAL Chi-restraints excluded: chain G residue 462 ARG Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 597 GLN 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 Chi-restraints excluded: chain I residue 162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 182 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 160 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN B 550 GLN B 597 GLN B 660 GLN B 663 ASN C 29 HIS D 73 ASN D 474 ASN D 484 ASN ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 574 GLN I 29 HIS I 112 GLN I 167 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5245 r_free = 0.5245 target = 0.207052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.176265 restraints weight = 46101.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.174954 restraints weight = 45852.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.176056 restraints weight = 37361.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.176188 restraints weight = 27139.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.176162 restraints weight = 27471.603| |-----------------------------------------------------------------------------| r_work (final): 0.4844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4938 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 16997 Z= 0.275 Angle : 1.041 15.626 23098 Z= 0.522 Chirality : 0.056 0.418 2703 Planarity : 0.007 0.067 2889 Dihedral : 11.452 111.481 2667 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 28.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 16.27 % Favored : 83.53 % Rotamer: Outliers : 10.10 % Allowed : 27.72 % Favored : 62.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.54 (0.16), residues: 2040 helix: -1.47 (0.24), residues: 345 sheet: -3.22 (0.21), residues: 399 loop : -3.60 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 279 TYR 0.052 0.003 TYR A 223 PHE 0.040 0.003 PHE G 367 TRP 0.043 0.003 TRP B 621 HIS 0.014 0.002 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00626 (16944) covalent geometry : angle 1.00366 (22974) SS BOND : bond 0.00830 ( 35) SS BOND : angle 2.04199 ( 70) hydrogen bonds : bond 0.06465 ( 405) hydrogen bonds : angle 7.26000 ( 1017) link_NAG-ASN : bond 0.00989 ( 18) link_NAG-ASN : angle 5.40024 ( 54) *********************** 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 357 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 168 time to evaluate : 0.635 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: A 233 LYS cc_start: 0.4863 (OUTLIER) cc_final: 0.4444 (tttt) REVERT: A 424 CYS cc_start: 0.2183 (OUTLIER) cc_final: 0.1960 (p) REVERT: A 458 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.5248 (mt) REVERT: A 483 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6226 (m-30) REVERT: A 498 LYS cc_start: 0.7690 (tttt) cc_final: 0.7361 (tptt) REVERT: B 627 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6639 (pttp) REVERT: C 145 THR cc_start: 0.7078 (OUTLIER) cc_final: 0.6391 (p) REVERT: D 245 CYS cc_start: 0.1536 (OUTLIER) cc_final: 0.0374 (p) REVERT: D 278 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6718 (pt) REVERT: D 354 LYS cc_start: 0.5381 (OUTLIER) cc_final: 0.5090 (pttp) REVERT: D 385 ARG cc_start: 0.3741 (mmm160) cc_final: 0.1836 (mpt180) REVERT: D 481 MET cc_start: 0.4347 (mmt) cc_final: 0.4073 (mtt) REVERT: D 484 ASN cc_start: -0.0816 (OUTLIER) cc_final: -0.2188 (t0) REVERT: E 605 CYS cc_start: 0.5491 (m) cc_final: 0.5031 (t) REVERT: F 36 ILE cc_start: -0.2640 (OUTLIER) cc_final: -0.3199 (mm) REVERT: G 78 HIS cc_start: 0.6020 (t70) cc_final: 0.5781 (t70) REVERT: G 106 MET cc_start: 0.6894 (ttp) cc_final: 0.6669 (ttp) REVERT: G 266 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.4661 (tp) REVERT: G 279 ARG cc_start: 0.5388 (OUTLIER) cc_final: 0.3441 (mtp85) REVERT: G 288 LYS cc_start: 0.3027 (OUTLIER) cc_final: 0.2151 (mmtm) REVERT: G 391 CYS cc_start: -0.0312 (OUTLIER) cc_final: -0.1553 (p) REVERT: G 424 CYS cc_start: 0.2561 (OUTLIER) cc_final: 0.0572 (t) REVERT: G 483 ASP cc_start: 0.6065 (OUTLIER) cc_final: 0.5862 (t0) REVERT: H 537 MET cc_start: 0.0916 (mtt) cc_final: -0.0063 (mtt) REVERT: H 578 TRP cc_start: 0.3090 (t-100) cc_final: 0.2797 (t-100) REVERT: H 605 CYS cc_start: 0.5134 (OUTLIER) cc_final: 0.3426 (p) REVERT: H 638 TRP cc_start: 0.6929 (OUTLIER) cc_final: 0.6486 (t-100) REVERT: I 94 GLU cc_start: 0.1505 (OUTLIER) cc_final: 0.1020 (tt0) REVERT: I 121 GLU cc_start: 0.4092 (OUTLIER) cc_final: 0.3583 (pm20) outliers start: 189 outliers final: 106 residues processed: 332 average time/residue: 0.1232 time to fit residues: 63.1159 Evaluate side-chains 266 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 139 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 424 CYS Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain 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 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 276 ILE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 354 LYS 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 480 ASP Chi-restraints excluded: chain D residue 484 ASN 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 590 ILE Chi-restraints excluded: chain E residue 596 ASP Chi-restraints excluded: chain E residue 645 TYR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 279 ARG Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 358 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 461 VAL Chi-restraints excluded: chain G residue 462 ARG Chi-restraints excluded: chain G residue 483 ASP Chi-restraints excluded: chain H residue 605 CYS Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 638 TRP Chi-restraints excluded: chain H residue 646 THR 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 177 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 185 optimal weight: 9.9990 chunk 146 optimal weight: 0.6980 chunk 161 optimal weight: 0.0050 chunk 112 optimal weight: 0.8980 chunk 194 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 174 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 154 optimal weight: 0.0370 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN G 255 HIS G 336 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 HIS ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 GLN I 167 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5315 r_free = 0.5315 target = 0.213061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.183327 restraints weight = 46118.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.182208 restraints weight = 39905.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.183452 restraints weight = 30925.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.183493 restraints weight = 22978.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.183404 restraints weight = 23973.808| |-----------------------------------------------------------------------------| r_work (final): 0.4939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4665 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16997 Z= 0.157 Angle : 0.844 12.433 23098 Z= 0.420 Chirality : 0.050 0.412 2703 Planarity : 0.005 0.061 2889 Dihedral : 9.830 108.010 2633 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.45 % Favored : 87.50 % Rotamer: Outliers : 7.69 % Allowed : 29.49 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.03 (0.16), residues: 2040 helix: -1.08 (0.25), residues: 354 sheet: -2.94 (0.22), residues: 411 loop : -3.23 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 279 TYR 0.017 0.002 TYR D 407 PHE 0.026 0.001 PHE G 59 TRP 0.042 0.002 TRP C 159 HIS 0.014 0.001 HIS I 29 Details of bonding type rmsd covalent geometry : bond 0.00329 (16944) covalent geometry : angle 0.81875 (22974) SS BOND : bond 0.00521 ( 35) SS BOND : angle 1.47405 ( 70) hydrogen bonds : bond 0.04621 ( 405) hydrogen bonds : angle 6.39387 ( 1017) link_NAG-ASN : bond 0.00803 ( 18) link_NAG-ASN : angle 4.08101 ( 54) *********************** 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 305 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 161 time to evaluate : 0.673 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 123 LYS cc_start: 0.4414 (OUTLIER) cc_final: 0.2475 (mtmm) REVERT: A 250 THR cc_start: 0.6493 (OUTLIER) cc_final: 0.6059 (m) REVERT: A 341 LYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5275 (mttt) REVERT: A 345 HIS cc_start: 0.5136 (OUTLIER) cc_final: 0.4728 (m-70) REVERT: A 396 LEU cc_start: 0.6605 (tp) cc_final: 0.6399 (tt) REVERT: A 498 LYS cc_start: 0.7168 (tttt) cc_final: 0.6838 (tptt) REVERT: B 537 MET cc_start: 0.5937 (mtt) cc_final: 0.5476 (mtt) REVERT: B 627 LYS cc_start: 0.6913 (mtmm) cc_final: 0.6684 (pttp) REVERT: C 74 LYS cc_start: 0.7249 (pttt) cc_final: 0.6717 (tmtt) REVERT: D 245 CYS cc_start: 0.1287 (OUTLIER) cc_final: -0.0189 (p) REVERT: D 278 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6238 (pt) REVERT: D 402 MET cc_start: 0.0718 (mmm) cc_final: 0.0499 (mmm) REVERT: E 599 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6426 (pp) REVERT: E 605 CYS cc_start: 0.5562 (m) cc_final: 0.4841 (t) REVERT: F 100 PHE cc_start: -0.1470 (OUTLIER) cc_final: -0.1722 (p90) REVERT: G 265 LEU cc_start: 0.8512 (mt) cc_final: 0.8301 (mp) REVERT: G 266 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4471 (tp) REVERT: G 391 CYS cc_start: -0.0254 (OUTLIER) cc_final: -0.1453 (p) REVERT: G 424 CYS cc_start: 0.2526 (OUTLIER) cc_final: 0.0673 (t) REVERT: G 432 MET cc_start: 0.2639 (mmm) cc_final: 0.2384 (mmm) REVERT: G 438 ARG cc_start: 0.2834 (OUTLIER) cc_final: 0.2335 (mmm160) REVERT: H 605 CYS cc_start: 0.4888 (OUTLIER) cc_final: 0.3546 (p) REVERT: H 638 TRP cc_start: 0.6867 (OUTLIER) cc_final: 0.6429 (t-100) REVERT: I 94 GLU cc_start: 0.1227 (OUTLIER) cc_final: 0.0930 (tt0) outliers start: 144 outliers final: 85 residues processed: 283 average time/residue: 0.1243 time to fit residues: 54.1192 Evaluate side-chains 239 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 139 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 266 LEU 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 303 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 341 LYS 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 402 MET 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 462 ARG Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain C residue 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 83 THR Chi-restraints excluded: chain C residue 95 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 205 SER Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 407 TYR Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 599 LEU 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 100 PHE 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 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 133 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 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 371 SER Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 424 CYS Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain H residue 545 THR Chi-restraints excluded: chain H residue 605 CYS 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 34 ASN Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 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 38 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 176 optimal weight: 0.0870 chunk 202 optimal weight: 20.0000 chunk 21 optimal weight: 0.0030 chunk 148 optimal weight: 0.6980 chunk 153 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.5368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5321 r_free = 0.5321 target = 0.213758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.183514 restraints weight = 45858.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.182114 restraints weight = 39548.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.183313 restraints weight = 31537.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.183393 restraints weight = 26192.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.183551 restraints weight = 24393.419| |-----------------------------------------------------------------------------| r_work (final): 0.4955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4657 moved from start: 0.6463 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= 0.140 Angle : 0.815 12.284 23098 Z= 0.404 Chirality : 0.049 0.436 2703 Planarity : 0.005 0.055 2889 Dihedral : 9.109 102.793 2609 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer: Outliers : 7.21 % Allowed : 29.54 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.79 (0.17), residues: 2040 helix: -0.52 (0.27), residues: 333 sheet: -2.82 (0.21), residues: 438 loop : -3.13 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 425 TYR 0.021 0.002 TYR A 223 PHE 0.024 0.001 PHE G 59 TRP 0.034 0.002 TRP G 41 HIS 0.012 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00301 (16944) covalent geometry : angle 0.78520 (22974) SS BOND : bond 0.00476 ( 35) SS BOND : angle 2.06385 ( 70) hydrogen bonds : bond 0.04212 ( 405) hydrogen bonds : angle 6.11041 ( 1017) link_NAG-ASN : bond 0.00745 ( 18) link_NAG-ASN : angle 4.01363 ( 54) *********************** 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 305 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 170 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.4373 (OUTLIER) cc_final: 0.2322 (mtmm) REVERT: A 266 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5282 (pp) REVERT: A 341 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.5341 (mttt) REVERT: A 345 HIS cc_start: 0.5070 (OUTLIER) cc_final: 0.4710 (m-70) REVERT: A 350 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.4779 (mtt180) REVERT: B 537 MET cc_start: 0.5868 (mtt) cc_final: 0.5481 (mtt) REVERT: B 627 LYS cc_start: 0.6986 (mtmm) cc_final: 0.6577 (pttp) REVERT: C 109 HIS cc_start: 0.2361 (OUTLIER) cc_final: 0.0808 (m170) REVERT: C 145 THR cc_start: 0.7034 (m) cc_final: 0.6507 (p) REVERT: D 245 CYS cc_start: 0.1645 (OUTLIER) cc_final: -0.0081 (p) REVERT: D 252 GLN cc_start: 0.6237 (tt0) cc_final: 0.5844 (tp-100) REVERT: D 278 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6264 (pt) REVERT: D 346 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: D 458 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6850 (tt) REVERT: D 509 ARG cc_start: 0.3592 (ptm-80) cc_final: 0.3347 (mmt180) REVERT: E 605 CYS cc_start: 0.5605 (m) cc_final: 0.4756 (t) REVERT: F 36 ILE cc_start: -0.2459 (mt) cc_final: -0.3323 (mm) REVERT: G 266 LEU cc_start: 0.5045 (OUTLIER) cc_final: 0.4428 (tp) REVERT: G 424 CYS cc_start: 0.2217 (OUTLIER) cc_final: 0.1903 (t) REVERT: G 438 ARG cc_start: 0.2676 (OUTLIER) cc_final: 0.2118 (mmm160) REVERT: G 440 MET cc_start: 0.0168 (tpt) cc_final: -0.0143 (tpt) REVERT: G 483 ASP cc_start: 0.6104 (OUTLIER) cc_final: 0.5837 (t70) REVERT: H 555 ILE cc_start: 0.0576 (mm) cc_final: 0.0279 (mt) REVERT: H 578 TRP cc_start: 0.3003 (t-100) cc_final: 0.2716 (t-100) REVERT: H 605 CYS cc_start: 0.5146 (OUTLIER) cc_final: 0.3747 (p) REVERT: H 638 TRP cc_start: 0.7055 (OUTLIER) cc_final: 0.6556 (t-100) REVERT: I 5 VAL cc_start: 0.5310 (t) cc_final: 0.4842 (m) REVERT: I 94 GLU cc_start: 0.1083 (OUTLIER) cc_final: 0.0785 (tt0) REVERT: I 121 GLU cc_start: 0.3771 (OUTLIER) cc_final: 0.3452 (pm20) outliers start: 135 outliers final: 84 residues processed: 283 average time/residue: 0.1229 time to fit residues: 54.6501 Evaluate side-chains 249 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 147 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 118 TRP Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 341 LYS 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 402 MET 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 483 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 655 ASP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain E residue 544 LEU 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 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 204 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 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 424 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 483 ASP Chi-restraints excluded: chain H residue 605 CYS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 89 optimal weight: 10.0000 chunk 67 optimal weight: 0.0050 chunk 200 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 119 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 358 HIS ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** 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 = 0.5317 r_free = 0.5317 target = 0.213227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.182065 restraints weight = 45657.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.180195 restraints weight = 41894.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.181815 restraints weight = 32121.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.182364 restraints weight = 24437.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.182458 restraints weight = 24804.042| |-----------------------------------------------------------------------------| r_work (final): 0.4922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4731 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16997 Z= 0.148 Angle : 0.821 14.823 23098 Z= 0.402 Chirality : 0.049 0.482 2703 Planarity : 0.005 0.058 2889 Dihedral : 9.503 99.331 2601 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.19 % Favored : 86.76 % Rotamer: Outliers : 7.05 % Allowed : 30.29 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.17), residues: 2040 helix: -0.54 (0.27), residues: 336 sheet: -2.59 (0.25), residues: 354 loop : -2.98 (0.15), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 425 TYR 0.026 0.002 TYR A 223 PHE 0.023 0.001 PHE G 59 TRP 0.055 0.002 TRP I 159 HIS 0.013 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00320 (16944) covalent geometry : angle 0.79027 (22974) SS BOND : bond 0.00402 ( 35) SS BOND : angle 1.77700 ( 70) hydrogen bonds : bond 0.04209 ( 405) hydrogen bonds : angle 6.02306 ( 1017) link_NAG-ASN : bond 0.00800 ( 18) link_NAG-ASN : angle 4.28740 ( 54) *********************** 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 292 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 160 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.4362 (OUTLIER) cc_final: 0.2386 (mtmm) REVERT: A 304 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.5838 (ptp-170) REVERT: A 310 ARG cc_start: 0.5880 (mpt180) cc_final: 0.4902 (tpm170) REVERT: A 341 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.5611 (mttt) REVERT: A 345 HIS cc_start: 0.5062 (OUTLIER) cc_final: 0.4684 (m-70) REVERT: A 350 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.4812 (mtt180) REVERT: A 482 ARG cc_start: 0.7600 (mtt90) cc_final: 0.6906 (mtp85) REVERT: B 537 MET cc_start: 0.5716 (mtt) cc_final: 0.5337 (mtt) REVERT: B 542 MET cc_start: 0.5132 (mmt) cc_final: 0.4838 (mmp) REVERT: B 627 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6802 (pptt) REVERT: C 109 HIS cc_start: 0.2472 (OUTLIER) cc_final: 0.0898 (m170) REVERT: D 110 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5817 (mtt) REVERT: D 245 CYS cc_start: 0.1219 (OUTLIER) cc_final: -0.0289 (p) REVERT: D 346 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: D 402 MET cc_start: 0.0085 (mmm) cc_final: -0.0320 (mmm) REVERT: D 445 ILE cc_start: 0.1274 (OUTLIER) cc_final: 0.0745 (mp) REVERT: D 458 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.7034 (tt) REVERT: E 605 CYS cc_start: 0.5494 (m) cc_final: 0.4874 (t) REVERT: F 36 ILE cc_start: -0.2638 (mt) cc_final: -0.3424 (mm) REVERT: G 266 LEU cc_start: 0.5121 (OUTLIER) cc_final: 0.4475 (tp) REVERT: G 391 CYS cc_start: -0.0294 (OUTLIER) cc_final: -0.0882 (p) REVERT: G 438 ARG cc_start: 0.2610 (OUTLIER) cc_final: 0.2083 (mmm160) REVERT: G 483 ASP cc_start: 0.6126 (OUTLIER) cc_final: 0.5877 (t70) REVERT: H 555 ILE cc_start: 0.0733 (mm) cc_final: 0.0129 (mt) REVERT: H 578 TRP cc_start: 0.3091 (t-100) cc_final: 0.2829 (t-100) REVERT: H 605 CYS cc_start: 0.5113 (OUTLIER) cc_final: 0.3726 (p) REVERT: H 638 TRP cc_start: 0.7028 (OUTLIER) cc_final: 0.6322 (t-100) REVERT: I 5 VAL cc_start: 0.5347 (t) cc_final: 0.4853 (m) REVERT: I 94 GLU cc_start: 0.0950 (OUTLIER) cc_final: 0.0602 (tt0) REVERT: I 121 GLU cc_start: 0.3755 (OUTLIER) cc_final: 0.3522 (pm20) outliers start: 132 outliers final: 88 residues processed: 268 average time/residue: 0.1270 time to fit residues: 51.9400 Evaluate side-chains 257 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 150 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 118 TRP 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 261 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 627 LYS 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 73 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 585 THR 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 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 204 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 371 SER Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 483 ASP Chi-restraints excluded: chain H residue 545 THR Chi-restraints excluded: chain H residue 605 CYS 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 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 178 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 200 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 115 optimal weight: 0.3980 chunk 68 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 78 optimal weight: 0.6980 chunk 113 optimal weight: 0.0370 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN A 334 GLN A 380 HIS ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 550 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.214960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.192649 restraints weight = 45790.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.195370 restraints weight = 60905.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.195714 restraints weight = 38326.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.195495 restraints weight = 32077.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.196369 restraints weight = 26198.045| |-----------------------------------------------------------------------------| r_work (final): 0.5111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4163 moved from start: 0.7205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16997 Z= 0.132 Angle : 0.785 12.314 23098 Z= 0.386 Chirality : 0.047 0.432 2703 Planarity : 0.005 0.055 2889 Dihedral : 9.333 110.808 2600 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.50 % Favored : 87.45 % Rotamer: Outliers : 6.20 % Allowed : 30.88 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.17), residues: 2040 helix: -0.54 (0.26), residues: 354 sheet: -2.30 (0.25), residues: 354 loop : -2.94 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 385 TYR 0.014 0.001 TYR B 593 PHE 0.024 0.001 PHE I 172 TRP 0.054 0.002 TRP I 159 HIS 0.008 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00286 (16944) covalent geometry : angle 0.76196 (22974) SS BOND : bond 0.00434 ( 35) SS BOND : angle 1.51142 ( 70) hydrogen bonds : bond 0.03757 ( 405) hydrogen bonds : angle 5.83573 ( 1017) link_NAG-ASN : bond 0.00701 ( 18) link_NAG-ASN : angle 3.72293 ( 54) *********************** 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 271 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 155 time to evaluate : 0.674 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 123 LYS cc_start: 0.4062 (OUTLIER) cc_final: 0.2052 (mtmm) REVERT: A 266 LEU cc_start: 0.5689 (OUTLIER) cc_final: 0.5243 (pp) REVERT: A 310 ARG cc_start: 0.5505 (mpt180) cc_final: 0.4830 (tpm170) REVERT: A 350 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.4807 (mtt180) REVERT: A 454 ASN cc_start: 0.6927 (p0) cc_final: 0.5851 (m-40) REVERT: A 455 ILE cc_start: 0.5852 (OUTLIER) cc_final: 0.5297 (mp) REVERT: A 482 ARG cc_start: 0.7426 (mtt90) cc_final: 0.6684 (mtp85) REVERT: B 537 MET cc_start: 0.5398 (mtt) cc_final: 0.5028 (mtt) REVERT: B 637 GLN cc_start: 0.6249 (pt0) cc_final: 0.5444 (tm-30) REVERT: C 109 HIS cc_start: 0.2408 (OUTLIER) cc_final: 0.0866 (m170) REVERT: D 245 CYS cc_start: 0.1020 (OUTLIER) cc_final: -0.0630 (p) REVERT: D 440 MET cc_start: 0.2720 (tmm) cc_final: 0.2493 (tmm) REVERT: D 445 ILE cc_start: 0.1274 (OUTLIER) cc_final: 0.0719 (mp) REVERT: E 542 MET cc_start: 0.5897 (mmm) cc_final: 0.4920 (mmt) REVERT: F 36 ILE cc_start: -0.2541 (mt) cc_final: -0.3355 (mm) REVERT: F 174 ILE cc_start: 0.2900 (OUTLIER) cc_final: 0.2624 (mm) REVERT: G 266 LEU cc_start: 0.4846 (OUTLIER) cc_final: 0.4343 (tp) REVERT: G 391 CYS cc_start: -0.0131 (OUTLIER) cc_final: -0.0670 (p) REVERT: G 438 ARG cc_start: 0.2606 (OUTLIER) cc_final: 0.2278 (mmm160) REVERT: H 578 TRP cc_start: 0.2718 (t-100) cc_final: 0.2459 (t-100) REVERT: H 605 CYS cc_start: 0.4687 (OUTLIER) cc_final: 0.3417 (p) REVERT: H 638 TRP cc_start: 0.6513 (OUTLIER) cc_final: 0.6142 (t-100) REVERT: I 5 VAL cc_start: 0.4925 (t) cc_final: 0.4448 (m) REVERT: I 94 GLU cc_start: 0.1472 (OUTLIER) cc_final: 0.1080 (tt0) outliers start: 116 outliers final: 77 residues processed: 255 average time/residue: 0.1293 time to fit residues: 50.9699 Evaluate side-chains 234 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 143 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 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 261 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 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 461 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 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 73 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain 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 225 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 309 THR 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 E residue 544 LEU Chi-restraints excluded: chain E residue 585 THR 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 F residue 174 ILE Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 277 ILE Chi-restraints excluded: chain G residue 297 SER Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 345 HIS Chi-restraints excluded: chain G residue 391 CYS Chi-restraints excluded: chain G residue 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 461 VAL Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 545 THR Chi-restraints excluded: chain H residue 605 CYS 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 83 THR Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 119 THR 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 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 198 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 chunk 184 optimal weight: 0.0870 chunk 74 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5326 r_free = 0.5326 target = 0.214005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.184336 restraints weight = 45762.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.183380 restraints weight = 38994.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.184945 restraints weight = 30792.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.184823 restraints weight = 23057.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.184959 restraints weight = 23365.210| |-----------------------------------------------------------------------------| r_work (final): 0.4970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4620 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16997 Z= 0.143 Angle : 0.803 12.167 23098 Z= 0.393 Chirality : 0.048 0.413 2703 Planarity : 0.005 0.058 2889 Dihedral : 9.154 107.870 2595 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.55 % Favored : 87.40 % Rotamer: Outliers : 6.36 % Allowed : 30.02 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.17), residues: 2040 helix: -0.38 (0.27), residues: 339 sheet: -2.20 (0.26), residues: 348 loop : -2.76 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 279 TYR 0.025 0.001 TYR A 223 PHE 0.021 0.002 PHE G 59 TRP 0.043 0.002 TRP I 159 HIS 0.009 0.001 HIS G 358 Details of bonding type rmsd covalent geometry : bond 0.00315 (16944) covalent geometry : angle 0.78075 (22974) SS BOND : bond 0.00456 ( 35) SS BOND : angle 1.60423 ( 70) hydrogen bonds : bond 0.03842 ( 405) hydrogen bonds : angle 5.81950 ( 1017) link_NAG-ASN : bond 0.00691 ( 18) link_NAG-ASN : angle 3.64054 ( 54) *********************** 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 271 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 152 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LYS cc_start: 0.4133 (OUTLIER) cc_final: 0.2133 (mtmm) REVERT: A 350 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.4775 (mtt180) REVERT: A 391 CYS cc_start: 0.1061 (OUTLIER) cc_final: -0.0628 (t) REVERT: A 482 ARG cc_start: 0.7610 (mtt90) cc_final: 0.7091 (mtp180) REVERT: A 508 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7246 (pttm) REVERT: B 537 MET cc_start: 0.5603 (mtt) cc_final: 0.5130 (mtt) REVERT: B 637 GLN cc_start: 0.6524 (pt0) cc_final: 0.5697 (tm-30) REVERT: C 109 HIS cc_start: 0.2581 (OUTLIER) cc_final: 0.1095 (m170) REVERT: D 245 CYS cc_start: 0.1192 (OUTLIER) cc_final: -0.0495 (p) REVERT: D 422 ILE cc_start: -0.1645 (OUTLIER) cc_final: -0.2086 (mp) REVERT: D 440 MET cc_start: 0.3069 (tmm) cc_final: 0.2854 (tmm) REVERT: D 445 ILE cc_start: 0.1422 (OUTLIER) cc_final: 0.0882 (mp) REVERT: E 542 MET cc_start: 0.6493 (mmm) cc_final: 0.5540 (mmt) REVERT: F 36 ILE cc_start: -0.2696 (mt) cc_final: -0.3097 (mt) REVERT: G 125 CYS cc_start: 0.1312 (OUTLIER) cc_final: 0.0404 (p) REVERT: G 377 ILE cc_start: 0.5109 (mp) cc_final: 0.4658 (mm) REVERT: G 391 CYS cc_start: 0.0351 (OUTLIER) cc_final: -0.0141 (p) REVERT: G 438 ARG cc_start: 0.2742 (OUTLIER) cc_final: 0.2385 (mmm160) REVERT: H 578 TRP cc_start: 0.2984 (t-100) cc_final: 0.2730 (t-100) REVERT: H 605 CYS cc_start: 0.5062 (OUTLIER) cc_final: 0.3702 (p) REVERT: H 638 TRP cc_start: 0.6971 (OUTLIER) cc_final: 0.6502 (t-100) REVERT: I 94 GLU cc_start: 0.1389 (OUTLIER) cc_final: 0.1010 (tt0) outliers start: 119 outliers final: 85 residues processed: 255 average time/residue: 0.1244 time to fit residues: 49.8867 Evaluate side-chains 239 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 140 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 266 LEU 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 347 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain 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 73 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain 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 255 HIS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 585 THR 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 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 204 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 250 THR 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 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 461 VAL Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain H residue 545 THR Chi-restraints excluded: chain H residue 605 CYS 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 24 LYS Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 GLU 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 62 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 1 optimal weight: 0.0970 chunk 181 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 58 optimal weight: 0.1980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 ASN ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN F 131 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 484 ASN ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5287 r_free = 0.5287 target = 0.210432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.179571 restraints weight = 45250.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.178610 restraints weight = 40394.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.180003 restraints weight = 31664.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.179878 restraints weight = 24600.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.179964 restraints weight = 25897.514| |-----------------------------------------------------------------------------| r_work (final): 0.4890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4801 moved from start: 0.7685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16997 Z= 0.192 Angle : 0.865 11.912 23098 Z= 0.430 Chirality : 0.050 0.410 2703 Planarity : 0.005 0.058 2889 Dihedral : 9.442 104.792 2593 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.73 % Favored : 86.23 % Rotamer: Outliers : 5.77 % Allowed : 31.14 % Favored : 63.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.17), residues: 2040 helix: -0.68 (0.26), residues: 345 sheet: -2.07 (0.24), residues: 384 loop : -2.79 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 279 TYR 0.044 0.002 TYR A 223 PHE 0.020 0.002 PHE G 59 TRP 0.056 0.002 TRP E 578 HIS 0.010 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00441 (16944) covalent geometry : angle 0.84375 (22974) SS BOND : bond 0.00587 ( 35) SS BOND : angle 1.85904 ( 70) hydrogen bonds : bond 0.04555 ( 405) hydrogen bonds : angle 6.08567 ( 1017) link_NAG-ASN : bond 0.00699 ( 18) link_NAG-ASN : angle 3.58776 ( 54) *********************** 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 251 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 143 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TYR cc_start: 0.6258 (p90) cc_final: 0.5960 (p90) REVERT: A 123 LYS cc_start: 0.4503 (OUTLIER) cc_final: 0.2345 (mtmm) REVERT: A 350 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.4406 (mtt180) REVERT: A 391 CYS cc_start: 0.1081 (OUTLIER) cc_final: -0.0770 (p) REVERT: C 109 HIS cc_start: 0.2584 (OUTLIER) cc_final: 0.0986 (m170) REVERT: D 245 CYS cc_start: 0.1344 (OUTLIER) cc_final: -0.0320 (p) REVERT: D 422 ILE cc_start: -0.1624 (OUTLIER) cc_final: -0.2105 (mp) REVERT: D 445 ILE cc_start: 0.1463 (OUTLIER) cc_final: 0.0951 (mp) REVERT: E 542 MET cc_start: 0.6399 (mmm) cc_final: 0.5478 (mmt) REVERT: F 36 ILE cc_start: -0.2357 (mt) cc_final: -0.2723 (mt) REVERT: F 172 PHE cc_start: -0.2020 (m-80) cc_final: -0.2227 (m-80) REVERT: G 125 CYS cc_start: 0.1425 (OUTLIER) cc_final: 0.0662 (p) REVERT: G 377 ILE cc_start: 0.4849 (mp) cc_final: 0.4450 (mm) REVERT: G 391 CYS cc_start: 0.0488 (OUTLIER) cc_final: 0.0041 (p) REVERT: G 438 ARG cc_start: 0.2850 (OUTLIER) cc_final: 0.2458 (mmm160) REVERT: H 605 CYS cc_start: 0.5141 (OUTLIER) cc_final: 0.3540 (p) REVERT: H 638 TRP cc_start: 0.6941 (OUTLIER) cc_final: 0.6646 (t-100) REVERT: I 94 GLU cc_start: 0.1435 (OUTLIER) cc_final: 0.1015 (tt0) outliers start: 108 outliers final: 81 residues processed: 234 average time/residue: 0.1196 time to fit residues: 43.5902 Evaluate side-chains 226 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 132 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 LEU 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 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 MET 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 585 THR 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 73 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 293 HIS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain E residue 544 LEU 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 131 GLN Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 250 THR 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 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 461 VAL Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain H residue 605 CYS Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 638 TRP Chi-restraints excluded: chain I residue 24 LYS 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 178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 36 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 170 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 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** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5303 r_free = 0.5303 target = 0.211778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.181701 restraints weight = 45362.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.180657 restraints weight = 39406.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.181689 restraints weight = 34083.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.181830 restraints weight = 25823.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.181916 restraints weight = 25798.767| |-----------------------------------------------------------------------------| r_work (final): 0.4918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4728 moved from start: 0.7888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16997 Z= 0.156 Angle : 0.841 21.520 23098 Z= 0.411 Chirality : 0.049 0.548 2703 Planarity : 0.005 0.059 2889 Dihedral : 9.154 102.457 2593 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.65 % Favored : 87.30 % Rotamer: Outliers : 5.07 % Allowed : 32.43 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.17), residues: 2040 helix: -0.56 (0.26), residues: 345 sheet: -2.05 (0.24), residues: 384 loop : -2.75 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 133 TYR 0.029 0.002 TYR A 223 PHE 0.021 0.002 PHE G 59 TRP 0.048 0.003 TRP F 159 HIS 0.009 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00353 (16944) covalent geometry : angle 0.80726 (22974) SS BOND : bond 0.00444 ( 35) SS BOND : angle 1.61379 ( 70) hydrogen bonds : bond 0.04123 ( 405) hydrogen bonds : angle 6.00096 ( 1017) link_NAG-ASN : bond 0.00922 ( 18) link_NAG-ASN : angle 4.65167 ( 54) ********************** 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: 95 poor density : 137 time to evaluate : 0.659 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: A 123 LYS cc_start: 0.4451 (OUTLIER) cc_final: 0.2469 (mtmm) REVERT: A 362 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7564 (mmtt) REVERT: A 391 CYS cc_start: 0.1292 (OUTLIER) cc_final: -0.0776 (p) REVERT: C 109 HIS cc_start: 0.2580 (OUTLIER) cc_final: 0.0976 (m170) REVERT: D 101 MET cc_start: 0.6212 (ttm) cc_final: 0.6000 (ttm) REVERT: D 245 CYS cc_start: 0.1704 (OUTLIER) cc_final: -0.0232 (p) REVERT: D 422 ILE cc_start: -0.1796 (OUTLIER) cc_final: -0.2215 (mp) REVERT: D 445 ILE cc_start: 0.1268 (OUTLIER) cc_final: 0.0778 (mp) REVERT: E 542 MET cc_start: 0.6361 (mmm) cc_final: 0.5460 (mmt) REVERT: F 36 ILE cc_start: -0.2542 (mt) cc_final: -0.2910 (mt) REVERT: G 125 CYS cc_start: 0.1453 (OUTLIER) cc_final: 0.0599 (p) REVERT: G 377 ILE cc_start: 0.4996 (mp) cc_final: 0.4617 (mm) REVERT: G 391 CYS cc_start: 0.0510 (OUTLIER) cc_final: 0.0088 (p) REVERT: G 438 ARG cc_start: 0.2893 (OUTLIER) cc_final: 0.2437 (mmm160) REVERT: H 605 CYS cc_start: 0.5218 (OUTLIER) cc_final: 0.3620 (p) REVERT: H 638 TRP cc_start: 0.7080 (OUTLIER) cc_final: 0.6707 (t-100) REVERT: I 94 GLU cc_start: 0.1330 (OUTLIER) cc_final: 0.0980 (tt0) outliers start: 95 outliers final: 78 residues processed: 220 average time/residue: 0.1198 time to fit residues: 41.7440 Evaluate side-chains 225 residues out of total 1875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 134 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 266 LEU 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 345 HIS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 MET 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 440 MET 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 585 THR Chi-restraints excluded: chain B residue 605 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 73 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 109 HIS Chi-restraints excluded: chain D residue 45 TYR Chi-restraints excluded: chain D residue 59 PHE Chi-restraints excluded: chain D residue 111 HIS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 255 HIS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 495 VAL 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 88 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 125 CYS Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 CYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 245 CYS Chi-restraints excluded: chain G residue 250 THR 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 391 CYS Chi-restraints excluded: chain G residue 430 ILE Chi-restraints excluded: chain G residue 436 VAL Chi-restraints excluded: chain G residue 438 ARG Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 496 GLU Chi-restraints excluded: chain H residue 605 CYS Chi-restraints excluded: chain H residue 610 ILE Chi-restraints excluded: chain H residue 638 TRP 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 178 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 121 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN ** G 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 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 = 0.5307 r_free = 0.5307 target = 0.212061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.182787 restraints weight = 45343.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.181468 restraints weight = 42490.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.182633 restraints weight = 34303.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.182811 restraints weight = 26754.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.182803 restraints weight = 28058.437| |-----------------------------------------------------------------------------| r_work (final): 0.4918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4684 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16997 Z= 0.149 Angle : 0.827 20.416 23098 Z= 0.404 Chirality : 0.049 0.533 2703 Planarity : 0.005 0.059 2889 Dihedral : 8.853 97.762 2592 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.94 % Favored : 87.01 % Rotamer: Outliers : 5.18 % Allowed : 32.32 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.17), residues: 2040 helix: -0.48 (0.26), residues: 345 sheet: -2.07 (0.24), residues: 390 loop : -2.72 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 425 TYR 0.031 0.002 TYR A 223 PHE 0.021 0.002 PHE G 59 TRP 0.051 0.002 TRP E 578 HIS 0.010 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00337 (16944) covalent geometry : angle 0.79525 (22974) SS BOND : bond 0.00407 ( 35) SS BOND : angle 1.47241 ( 70) hydrogen bonds : bond 0.04033 ( 405) hydrogen bonds : angle 5.92507 ( 1017) link_NAG-ASN : bond 0.00876 ( 18) link_NAG-ASN : angle 4.55511 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4387.48 seconds wall clock time: 76 minutes 17.59 seconds (4577.59 seconds total)