Starting phenix.real_space_refine on Mon Jun 16 20:50:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnk_26012/06_2025/7tnk_26012.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnk_26012/06_2025/7tnk_26012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnk_26012/06_2025/7tnk_26012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnk_26012/06_2025/7tnk_26012.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnk_26012/06_2025/7tnk_26012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnk_26012/06_2025/7tnk_26012.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12281 2.51 5 N 3064 2.21 5 O 3449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18934 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4783 Classifications: {'peptide': 615} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 598} Chain breaks: 3 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4688 Classifications: {'peptide': 602} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 586} Chain breaks: 4 Chain: "C" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4669 Classifications: {'peptide': 599} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 583} Chain breaks: 4 Chain: "D" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4688 Classifications: {'peptide': 602} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 586} Chain breaks: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.50, per 1000 atoms: 0.55 Number of scatterers: 18934 At special positions: 0 Unit cell: (125.33, 114.54, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 136 16.00 O 3449 8.00 N 3064 7.00 C 12281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 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 Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 2.2 seconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 27 sheets defined 54.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.850A pdb=" N GLU A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.672A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET A 527 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.712A pdb=" N THR A 568 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.583A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 625 removed outlier: 3.766A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 removed outlier: 4.012A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.561A pdb=" N ASP A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.819A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.886A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.528A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 removed outlier: 3.866A pdb=" N LYS A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 820 removed outlier: 4.015A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 813 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1029 removed outlier: 3.504A pdb=" N PHE A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1103 Processing helix chain 'A' and resid 1104 through 1126 removed outlier: 4.024A pdb=" N CYS A1120 " --> pdb=" O MET A1116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A1121 " --> pdb=" O GLY A1117 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A1122 " --> pdb=" O GLY A1118 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A1125 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A1126 " --> pdb=" O ALA A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1158 removed outlier: 3.854A pdb=" N SER A1136 " --> pdb=" O ASN A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1206 removed outlier: 3.656A pdb=" N GLY A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A1189 " --> pdb=" O SER A1185 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A1202 " --> pdb=" O HIS A1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.971A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 424 through 437 Processing helix chain 'B' and resid 461 through 470 removed outlier: 3.527A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 522 through 546 removed outlier: 3.717A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.520A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.842A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.864A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 675 removed outlier: 3.841A pdb=" N ARG B 675 " --> pdb=" O TRP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.956A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.754A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.857A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 756 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 792 through 820 removed outlier: 3.600A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1029 removed outlier: 3.918A pdb=" N SER B1021 " --> pdb=" O PHE B1017 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B1026 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B1028 " --> pdb=" O THR B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1089 removed outlier: 4.008A pdb=" N ASP B1087 " --> pdb=" O GLU B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1103 removed outlier: 3.689A pdb=" N ARG B1098 " --> pdb=" O GLU B1094 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B1099 " --> pdb=" O TYR B1095 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B1100 " --> pdb=" O PHE B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1127 removed outlier: 3.745A pdb=" N LEU B1114 " --> pdb=" O SER B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1161 removed outlier: 3.554A pdb=" N PHE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B1143 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B1144 " --> pdb=" O PHE B1140 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B1155 " --> pdb=" O GLY B1151 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B1159 " --> pdb=" O TYR B1155 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1192 removed outlier: 3.517A pdb=" N PHE B1186 " --> pdb=" O GLY B1182 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B1189 " --> pdb=" O SER B1185 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1204 removed outlier: 3.683A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS B1198 " --> pdb=" O VAL B1194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B1199 " --> pdb=" O LEU B1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 1204 through 1209 removed outlier: 3.575A pdb=" N THR B1208 " --> pdb=" O HIS B1204 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.518A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.805A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 544 removed outlier: 3.668A pdb=" N MET C 527 " --> pdb=" O TYR C 523 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 3.857A pdb=" N THR C 568 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN C 569 " --> pdb=" O GLU C 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 565 through 569' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 596 through 630 removed outlier: 3.570A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.869A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 4.103A pdb=" N MET C 670 " --> pdb=" O VAL C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 removed outlier: 3.510A pdb=" N ALA C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 694 " --> pdb=" O VAL C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.746A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.903A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 820 removed outlier: 4.188A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS C 815 " --> pdb=" O LEU C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1028 removed outlier: 3.617A pdb=" N LEU C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE C1017 " --> pdb=" O THR C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1093 through 1103 removed outlier: 3.610A pdb=" N ALA C1099 " --> pdb=" O TYR C1095 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C1102 " --> pdb=" O ARG C1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1123 removed outlier: 3.625A pdb=" N VAL C1111 " --> pdb=" O PRO C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1158 removed outlier: 3.578A pdb=" N ILE C1139 " --> pdb=" O LEU C1135 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1179 through 1208 removed outlier: 3.573A pdb=" N LEU C1195 " --> pdb=" O MET C1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.736A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.550A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 522 through 545 removed outlier: 4.209A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.668A pdb=" N PHE D 584 " --> pdb=" O SER D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.874A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 640 Processing helix chain 'D' and resid 653 through 662 removed outlier: 4.016A pdb=" N ARG D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER D 662 " --> pdb=" O PHE D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.830A pdb=" N THR D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.764A pdb=" N GLY D 689 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 694 " --> pdb=" O VAL D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 removed outlier: 3.522A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.633A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 749 " --> pdb=" O PRO D 745 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN D 756 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 792 through 819 removed outlier: 4.021A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1028 removed outlier: 3.746A pdb=" N THR D1024 " --> pdb=" O PHE D1020 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D1025 " --> pdb=" O SER D1021 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D1028 " --> pdb=" O THR D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1089 removed outlier: 3.746A pdb=" N TYR D1088 " --> pdb=" O ASP D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1093 through 1103 removed outlier: 3.643A pdb=" N VAL D1100 " --> pdb=" O PHE D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1123 removed outlier: 4.011A pdb=" N SER D1110 " --> pdb=" O PHE D1106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D1111 " --> pdb=" O PRO D1107 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS D1120 " --> pdb=" O MET D1116 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D1121 " --> pdb=" O GLY D1117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA D1122 " --> pdb=" O GLY D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1161 removed outlier: 4.175A pdb=" N PHE D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D1142 " --> pdb=" O GLY D1138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D1147 " --> pdb=" O SER D1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 1176 through 1209 removed outlier: 3.677A pdb=" N TYR D1180 " --> pdb=" O GLY D1176 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D1186 " --> pdb=" O GLY D1182 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D1195 " --> pdb=" O MET D1191 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D1209 " --> pdb=" O LYS D1205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 442 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 406 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.894A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.265A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1033 through 1034 Processing sheet with id=AA7, first strand: chain 'A' and resid 1058 through 1059 removed outlier: 3.571A pdb=" N CYS A1066 " --> pdb=" O HIS A1059 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 442 through 444 removed outlier: 6.299A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.054A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.543A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1057 through 1060 Processing sheet with id=AB5, first strand: chain 'B' and resid 1065 through 1066 Processing sheet with id=AB6, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AB7, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.745A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 454 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE C 459 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.662A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 646 through 649 removed outlier: 6.527A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1058 through 1059 Processing sheet with id=AC3, first strand: chain 'D' and resid 441 through 444 Processing sheet with id=AC4, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.540A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC7, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.000A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.429A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 1057 through 1060 removed outlier: 3.864A pdb=" N LEU D1033 " --> pdb=" O SER D1060 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2682 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: 5.37 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5633 1.34 - 1.46: 4459 1.46 - 1.58: 9039 1.58 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19359 Sorted by residual: bond pdb=" CA ASP D1091 " pdb=" CB ASP D1091 " ideal model delta sigma weight residual 1.524 1.557 -0.034 1.30e-02 5.92e+03 6.72e+00 bond pdb=" C SER A 631 " pdb=" N PRO A 632 " ideal model delta sigma weight residual 1.333 1.369 -0.036 1.44e-02 4.82e+03 6.25e+00 bond pdb=" N ASN A1053 " pdb=" CA ASN A1053 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.02e+00 bond pdb=" C ASP B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.337 1.358 -0.021 9.80e-03 1.04e+04 4.64e+00 bond pdb=" N3 CYZ A1302 " pdb=" S2 CYZ A1302 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.38e+00 ... (remaining 19354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 25706 3.05 - 6.11: 382 6.11 - 9.16: 59 9.16 - 12.21: 5 12.21 - 15.27: 2 Bond angle restraints: 26154 Sorted by residual: angle pdb=" C VAL A1056 " pdb=" N MET A1057 " pdb=" CA MET A1057 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" C GLU B 772 " pdb=" N CYS B 773 " pdb=" CA CYS B 773 " ideal model delta sigma weight residual 121.54 132.22 -10.68 1.91e+00 2.74e-01 3.13e+01 angle pdb=" N ASN B1132 " pdb=" CA ASN B1132 " pdb=" C ASN B1132 " ideal model delta sigma weight residual 113.61 105.90 7.71 1.50e+00 4.44e-01 2.64e+01 angle pdb=" C GLU C1089 " pdb=" N ALA C1090 " pdb=" CA ALA C1090 " ideal model delta sigma weight residual 120.44 127.06 -6.62 1.30e+00 5.92e-01 2.60e+01 angle pdb=" C GLY C 771 " pdb=" N GLU C 772 " pdb=" CA GLU C 772 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 ... (remaining 26149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.41: 11066 24.41 - 48.82: 352 48.82 - 73.23: 15 73.23 - 97.64: 9 97.64 - 122.05: 7 Dihedral angle restraints: 11449 sinusoidal: 4522 harmonic: 6927 Sorted by residual: dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 -179.42 -87.58 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CA ALA A 775 " pdb=" C ALA A 775 " pdb=" N LYS A 776 " pdb=" CA LYS A 776 " ideal model delta harmonic sigma weight residual 180.00 132.71 47.29 0 5.00e+00 4.00e-02 8.94e+01 dihedral pdb=" CA LYS B 509 " pdb=" C LYS B 509 " pdb=" N SER B 510 " pdb=" CA SER B 510 " ideal model delta harmonic sigma weight residual -180.00 -135.48 -44.52 0 5.00e+00 4.00e-02 7.93e+01 ... (remaining 11446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2185 0.052 - 0.105: 584 0.105 - 0.157: 129 0.157 - 0.209: 19 0.209 - 0.261: 8 Chirality restraints: 2925 Sorted by residual: chirality pdb=" C8 CYZ D1301 " pdb=" C1 CYZ D1301 " pdb=" N1 CYZ D1301 " pdb=" N2 CYZ D1301 " both_signs ideal model delta sigma weight residual False 2.20 2.46 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE B1079 " pdb=" CA ILE B1079 " pdb=" CG1 ILE B1079 " pdb=" CG2 ILE B1079 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C8 CYZ C1301 " pdb=" C1 CYZ C1301 " pdb=" N1 CYZ C1301 " pdb=" N2 CYZ C1301 " both_signs ideal model delta sigma weight residual False 2.20 2.45 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2922 not shown) Planarity restraints: 3209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 509 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C LYS B 509 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS B 509 " 0.023 2.00e-02 2.50e+03 pdb=" N SER B 510 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D1106 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO D1107 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D1107 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D1107 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 744 " -0.050 5.00e-02 4.00e+02 7.41e-02 8.80e+00 pdb=" N PRO B 745 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " -0.042 5.00e-02 4.00e+02 ... (remaining 3206 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 4413 2.78 - 3.31: 17656 3.31 - 3.84: 30758 3.84 - 4.37: 36528 4.37 - 4.90: 60286 Nonbonded interactions: 149641 Sorted by model distance: nonbonded pdb=" O PHE D1106 " pdb=" OG SER D1147 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR C 643 " pdb=" OD1 ASP D 777 " model vdw 2.256 3.040 nonbonded pdb=" O GLU A 637 " pdb=" OG SER A 640 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR B1065 " pdb=" O LYS B1077 " model vdw 2.280 3.040 nonbonded pdb=" O ILE D1025 " pdb=" OG1 THR D1029 " model vdw 2.292 3.040 ... (remaining 149636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 564 or resid 566 through 1042 or resid 1056 th \ rough 1161 or resid 1169 through 1208 or resid 1302)) selection = (chain 'B' and (resid 394 through 549 or resid 564 or resid 566 through 1208 or \ resid 1301)) selection = chain 'C' selection = (chain 'D' and (resid 394 through 549 or resid 564 or resid 566 through 1208 or \ resid 1301)) } 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: 2.900 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 39.190 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 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 : 0.005 0.079 19371 Z= 0.248 Angle : 1.012 15.267 26178 Z= 0.572 Chirality : 0.052 0.261 2925 Planarity : 0.006 0.076 3209 Dihedral : 11.811 122.047 6997 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 0.40 % Allowed : 4.36 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.12), residues: 2380 helix: -3.73 (0.07), residues: 1242 sheet: -1.99 (0.38), residues: 162 loop : -2.69 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A1177 HIS 0.006 0.001 HIS B1204 PHE 0.038 0.002 PHE C1082 TYR 0.042 0.003 TYR C1031 ARG 0.008 0.001 ARG D 628 Details of bonding type rmsd hydrogen bonds : bond 0.30382 ( 918) hydrogen bonds : angle 9.77342 ( 2682) SS BOND : bond 0.00360 ( 12) SS BOND : angle 1.59374 ( 24) covalent geometry : bond 0.00523 (19359) covalent geometry : angle 1.01123 (26154) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 658 time to evaluate : 1.983 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 453 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7676 (ttp80) REVERT: A 573 ILE cc_start: 0.7831 (pt) cc_final: 0.7518 (mt) REVERT: A 610 LEU cc_start: 0.9201 (tp) cc_final: 0.8990 (tp) REVERT: A 644 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7622 (mp0) REVERT: A 670 MET cc_start: 0.8182 (mtp) cc_final: 0.7981 (mtt) REVERT: A 730 LYS cc_start: 0.8202 (mttt) cc_final: 0.7874 (mmmm) REVERT: A 800 VAL cc_start: 0.9121 (t) cc_final: 0.8892 (p) REVERT: A 1020 PHE cc_start: 0.7907 (t80) cc_final: 0.7352 (t80) REVERT: A 1025 ILE cc_start: 0.9065 (mm) cc_final: 0.8864 (mt) REVERT: A 1031 TYR cc_start: 0.6504 (p90) cc_final: 0.5637 (p90) REVERT: A 1155 TYR cc_start: 0.8062 (t80) cc_final: 0.7709 (t80) REVERT: A 1177 TRP cc_start: 0.5743 (p-90) cc_final: 0.4416 (m-10) REVERT: A 1190 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8612 (mm-30) REVERT: A 1191 MET cc_start: 0.7682 (tpt) cc_final: 0.7169 (mmt) REVERT: A 1205 LYS cc_start: 0.7558 (mtmt) cc_final: 0.6999 (tptp) REVERT: B 399 THR cc_start: 0.8625 (p) cc_final: 0.8388 (t) REVERT: B 425 CYS cc_start: 0.8636 (m) cc_final: 0.8075 (p) REVERT: B 428 LEU cc_start: 0.8694 (tp) cc_final: 0.8454 (tp) REVERT: B 434 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7876 (tttm) REVERT: B 444 ILE cc_start: 0.8093 (mm) cc_final: 0.7538 (mt) REVERT: B 474 ILE cc_start: 0.9096 (tt) cc_final: 0.8761 (mm) REVERT: B 498 LEU cc_start: 0.8975 (pt) cc_final: 0.8654 (pt) REVERT: B 527 MET cc_start: 0.7366 (ttt) cc_final: 0.6908 (tpt) REVERT: B 536 VAL cc_start: 0.8177 (t) cc_final: 0.5901 (p) REVERT: B 586 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7721 (mm-40) REVERT: B 600 ILE cc_start: 0.8871 (mt) cc_final: 0.8585 (mt) REVERT: B 605 TRP cc_start: 0.8307 (t-100) cc_final: 0.7487 (t-100) REVERT: B 609 THR cc_start: 0.9033 (p) cc_final: 0.8691 (t) REVERT: B 697 LYS cc_start: 0.6121 (mmtp) cc_final: 0.5609 (ptmt) REVERT: B 766 TRP cc_start: 0.5977 (t-100) cc_final: 0.4915 (t-100) REVERT: B 800 VAL cc_start: 0.9457 (t) cc_final: 0.9180 (p) REVERT: B 1003 PHE cc_start: 0.3351 (m-10) cc_final: 0.3129 (m-80) REVERT: B 1011 LEU cc_start: 0.8421 (tp) cc_final: 0.8118 (tt) REVERT: B 1181 PHE cc_start: 0.5888 (m-10) cc_final: 0.5527 (m-80) REVERT: B 1186 PHE cc_start: 0.7464 (t80) cc_final: 0.6942 (t80) REVERT: B 1191 MET cc_start: 0.8126 (mtp) cc_final: 0.7620 (mtm) REVERT: C 438 PHE cc_start: 0.7204 (p90) cc_final: 0.5703 (p90) REVERT: C 503 MET cc_start: 0.8424 (ttp) cc_final: 0.7850 (ttp) REVERT: C 511 LYS cc_start: 0.7518 (pmmt) cc_final: 0.6870 (mptt) REVERT: C 528 CYS cc_start: 0.8440 (m) cc_final: 0.7905 (m) REVERT: C 537 SER cc_start: 0.9190 (p) cc_final: 0.8673 (t) REVERT: C 585 MET cc_start: 0.8843 (mmt) cc_final: 0.8115 (mmt) REVERT: C 629 MET cc_start: 0.8386 (mtp) cc_final: 0.7629 (tmm) REVERT: C 702 TYR cc_start: 0.8041 (t80) cc_final: 0.7679 (t80) REVERT: C 764 ASN cc_start: 0.8181 (m-40) cc_final: 0.7872 (m-40) REVERT: C 1009 MET cc_start: 0.8701 (tpp) cc_final: 0.8473 (tpt) REVERT: C 1030 ASP cc_start: 0.6674 (p0) cc_final: 0.6424 (m-30) REVERT: C 1064 ARG cc_start: 0.7313 (mpp80) cc_final: 0.6554 (ttt180) REVERT: C 1141 PHE cc_start: 0.8818 (m-10) cc_final: 0.8550 (m-80) REVERT: C 1153 ILE cc_start: 0.9546 (mt) cc_final: 0.9205 (mm) REVERT: C 1180 TYR cc_start: 0.8577 (m-80) cc_final: 0.8124 (m-10) REVERT: D 431 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7738 (mm-30) REVERT: D 434 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8308 (mtpt) REVERT: D 489 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8192 (pp) REVERT: D 503 MET cc_start: 0.8169 (ttm) cc_final: 0.7543 (ptm) REVERT: D 505 LYS cc_start: 0.7491 (ttmt) cc_final: 0.7290 (pptt) REVERT: D 527 MET cc_start: 0.7993 (ptp) cc_final: 0.7694 (mtt) REVERT: D 537 SER cc_start: 0.8796 (p) cc_final: 0.8078 (t) REVERT: D 541 PHE cc_start: 0.8441 (t80) cc_final: 0.8156 (t80) REVERT: D 573 ILE cc_start: 0.9407 (tp) cc_final: 0.9177 (tt) REVERT: D 580 SER cc_start: 0.8574 (m) cc_final: 0.8138 (m) REVERT: D 601 VAL cc_start: 0.9504 (t) cc_final: 0.9297 (p) REVERT: D 629 MET cc_start: 0.5223 (pmt) cc_final: 0.4838 (mmm) REVERT: D 713 GLU cc_start: 0.7875 (tt0) cc_final: 0.7624 (tm-30) REVERT: D 714 GLN cc_start: 0.8376 (mm110) cc_final: 0.7865 (mm110) REVERT: D 752 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8675 (tptt) REVERT: D 1038 VAL cc_start: 0.7192 (t) cc_final: 0.6779 (m) REVERT: D 1062 LEU cc_start: 0.4783 (tp) cc_final: 0.4542 (tp) REVERT: D 1131 HIS cc_start: 0.6296 (m90) cc_final: 0.5989 (m90) REVERT: D 1134 ILE cc_start: 0.6307 (mp) cc_final: 0.6097 (mm) REVERT: D 1204 HIS cc_start: 0.7640 (m170) cc_final: 0.7152 (t-170) REVERT: D 1205 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7489 (mttm) outliers start: 8 outliers final: 0 residues processed: 662 average time/residue: 0.3199 time to fit residues: 317.4130 Evaluate side-chains 402 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 401 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 72 optimal weight: 0.4980 chunk 114 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN B 575 ASN B 714 GLN B1204 HIS C 418 ASN C 586 GLN C 619 ASN C 791 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1171 ASN C1204 HIS D 435 HIS D 587 GLN D 642 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1131 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082809 restraints weight = 62191.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.085019 restraints weight = 38472.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.086588 restraints weight = 27044.033| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19371 Z= 0.136 Angle : 0.626 8.095 26178 Z= 0.336 Chirality : 0.041 0.144 2925 Planarity : 0.005 0.084 3209 Dihedral : 8.505 103.850 2716 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.20 % Allowed : 3.27 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.15), residues: 2380 helix: -1.18 (0.12), residues: 1282 sheet: -1.57 (0.40), residues: 155 loop : -2.17 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1177 HIS 0.005 0.001 HIS B1059 PHE 0.024 0.001 PHE C 682 TYR 0.021 0.001 TYR A 673 ARG 0.011 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.05318 ( 918) hydrogen bonds : angle 4.86997 ( 2682) SS BOND : bond 0.00305 ( 12) SS BOND : angle 1.60671 ( 24) covalent geometry : bond 0.00285 (19359) covalent geometry : angle 0.62459 (26154) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 545 time to evaluate : 2.015 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 537 SER cc_start: 0.9066 (m) cc_final: 0.8850 (t) REVERT: A 543 VAL cc_start: 0.9317 (t) cc_final: 0.9090 (p) REVERT: A 708 MET cc_start: 0.8314 (mmt) cc_final: 0.8111 (mmt) REVERT: A 728 ASP cc_start: 0.8208 (p0) cc_final: 0.7717 (p0) REVERT: A 808 LEU cc_start: 0.8881 (tp) cc_final: 0.8600 (mm) REVERT: A 1004 ASP cc_start: 0.7784 (t0) cc_final: 0.7305 (m-30) REVERT: A 1007 VAL cc_start: 0.8809 (t) cc_final: 0.8530 (t) REVERT: A 1020 PHE cc_start: 0.7622 (t80) cc_final: 0.7270 (t80) REVERT: A 1025 ILE cc_start: 0.9045 (mm) cc_final: 0.8822 (mt) REVERT: A 1177 TRP cc_start: 0.5791 (p-90) cc_final: 0.5545 (p-90) REVERT: A 1179 PHE cc_start: 0.8650 (t80) cc_final: 0.7929 (t80) REVERT: A 1191 MET cc_start: 0.7604 (tpt) cc_final: 0.7155 (mmt) REVERT: B 399 THR cc_start: 0.8803 (p) cc_final: 0.8566 (t) REVERT: B 434 LYS cc_start: 0.8190 (ptpt) cc_final: 0.7978 (tptp) REVERT: B 444 ILE cc_start: 0.8199 (mm) cc_final: 0.7854 (mt) REVERT: B 474 ILE cc_start: 0.9069 (tt) cc_final: 0.8867 (mm) REVERT: B 481 ILE cc_start: 0.7096 (mm) cc_final: 0.6816 (mm) REVERT: B 498 LEU cc_start: 0.8581 (pt) cc_final: 0.8354 (pt) REVERT: B 527 MET cc_start: 0.7173 (ttt) cc_final: 0.6606 (tpt) REVERT: B 540 LEU cc_start: 0.9208 (tt) cc_final: 0.8938 (tt) REVERT: B 586 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8176 (mm-40) REVERT: B 684 ARG cc_start: 0.6658 (ptp90) cc_final: 0.5990 (mmm160) REVERT: B 697 LYS cc_start: 0.6296 (mmtp) cc_final: 0.5662 (ptmm) REVERT: B 766 TRP cc_start: 0.5754 (t-100) cc_final: 0.5072 (t-100) REVERT: B 768 TYR cc_start: 0.7987 (m-10) cc_final: 0.7462 (m-80) REVERT: B 1003 PHE cc_start: 0.3508 (m-10) cc_final: 0.3275 (m-80) REVERT: B 1188 ILE cc_start: 0.8423 (mm) cc_final: 0.8156 (tt) REVERT: B 1191 MET cc_start: 0.7849 (mtp) cc_final: 0.7589 (tpp) REVERT: C 406 VAL cc_start: 0.9287 (t) cc_final: 0.8749 (m) REVERT: C 528 CYS cc_start: 0.7954 (m) cc_final: 0.7631 (m) REVERT: C 585 MET cc_start: 0.8893 (mmt) cc_final: 0.8232 (mmt) REVERT: C 606 TRP cc_start: 0.8336 (m-10) cc_final: 0.8066 (m-10) REVERT: C 629 MET cc_start: 0.8132 (mtp) cc_final: 0.7609 (tmm) REVERT: C 639 LEU cc_start: 0.8736 (tp) cc_final: 0.8396 (tp) REVERT: C 760 ASP cc_start: 0.8268 (t70) cc_final: 0.7966 (t0) REVERT: C 764 ASN cc_start: 0.8174 (m-40) cc_final: 0.7927 (t0) REVERT: C 1030 ASP cc_start: 0.6590 (p0) cc_final: 0.6243 (m-30) REVERT: C 1062 LEU cc_start: 0.7613 (tp) cc_final: 0.6724 (pt) REVERT: C 1064 ARG cc_start: 0.7046 (mpp80) cc_final: 0.6348 (ttt-90) REVERT: C 1112 ILE cc_start: 0.8527 (mm) cc_final: 0.8320 (mm) REVERT: C 1153 ILE cc_start: 0.9300 (mt) cc_final: 0.9014 (mm) REVERT: C 1175 TYR cc_start: 0.6810 (m-80) cc_final: 0.6594 (m-80) REVERT: C 1180 TYR cc_start: 0.8259 (m-80) cc_final: 0.8045 (m-80) REVERT: C 1187 ILE cc_start: 0.9377 (mt) cc_final: 0.9094 (mt) REVERT: D 431 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7871 (mm-30) REVERT: D 434 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8182 (mtpt) REVERT: D 509 LYS cc_start: 0.6503 (ptpp) cc_final: 0.6054 (mmpt) REVERT: D 625 THR cc_start: 0.8655 (m) cc_final: 0.8252 (p) REVERT: D 713 GLU cc_start: 0.8203 (tt0) cc_final: 0.7890 (tm-30) REVERT: D 714 GLN cc_start: 0.8488 (mm110) cc_final: 0.7718 (mm-40) REVERT: D 752 LYS cc_start: 0.8969 (ttmt) cc_final: 0.7951 (tptt) REVERT: D 1062 LEU cc_start: 0.5004 (tp) cc_final: 0.4613 (tp) REVERT: D 1131 HIS cc_start: 0.6450 (m-70) cc_final: 0.6072 (m90) outliers start: 4 outliers final: 0 residues processed: 547 average time/residue: 0.3020 time to fit residues: 260.2709 Evaluate side-chains 378 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 27 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN A 619 ASN A 764 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 791 ASN C1008 GLN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.100673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.083182 restraints weight = 62541.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.085541 restraints weight = 38090.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.087162 restraints weight = 26426.143| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19371 Z= 0.122 Angle : 0.579 7.196 26178 Z= 0.309 Chirality : 0.041 0.146 2925 Planarity : 0.004 0.069 3209 Dihedral : 7.883 97.971 2716 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.16), residues: 2380 helix: -0.05 (0.14), residues: 1284 sheet: -1.41 (0.41), residues: 150 loop : -2.00 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1032 HIS 0.008 0.001 HIS B1204 PHE 0.021 0.001 PHE B1179 TYR 0.023 0.001 TYR A 711 ARG 0.006 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 918) hydrogen bonds : angle 4.39600 ( 2682) SS BOND : bond 0.00399 ( 12) SS BOND : angle 1.22690 ( 24) covalent geometry : bond 0.00259 (19359) covalent geometry : angle 0.57822 (26154) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 2.104 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 498 LEU cc_start: 0.8893 (pp) cc_final: 0.8485 (pp) REVERT: A 503 MET cc_start: 0.6993 (tmm) cc_final: 0.6673 (tmm) REVERT: A 543 VAL cc_start: 0.9340 (t) cc_final: 0.9139 (p) REVERT: A 808 LEU cc_start: 0.8744 (tp) cc_final: 0.8533 (mm) REVERT: A 1004 ASP cc_start: 0.7844 (t0) cc_final: 0.7326 (m-30) REVERT: A 1007 VAL cc_start: 0.8764 (t) cc_final: 0.8534 (t) REVERT: A 1025 ILE cc_start: 0.8889 (mm) cc_final: 0.8605 (mt) REVERT: A 1032 TRP cc_start: 0.7436 (m100) cc_final: 0.6595 (m100) REVERT: A 1062 LEU cc_start: 0.7057 (mp) cc_final: 0.6590 (pt) REVERT: A 1190 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8390 (mm-30) REVERT: A 1191 MET cc_start: 0.7743 (tpt) cc_final: 0.7270 (mmt) REVERT: B 444 ILE cc_start: 0.8139 (mm) cc_final: 0.7798 (mt) REVERT: B 474 ILE cc_start: 0.9129 (tt) cc_final: 0.8711 (mm) REVERT: B 527 MET cc_start: 0.7474 (ttt) cc_final: 0.6373 (tpt) REVERT: B 540 LEU cc_start: 0.9214 (tt) cc_final: 0.8961 (tt) REVERT: B 684 ARG cc_start: 0.6743 (ptp90) cc_final: 0.6019 (mmm160) REVERT: B 697 LYS cc_start: 0.6222 (mmtp) cc_final: 0.5670 (ptmm) REVERT: B 766 TRP cc_start: 0.5792 (t-100) cc_final: 0.5094 (t-100) REVERT: B 768 TYR cc_start: 0.8055 (m-10) cc_final: 0.7525 (m-80) REVERT: B 1005 ARG cc_start: 0.4617 (ptm160) cc_final: 0.4404 (ptm160) REVERT: C 406 VAL cc_start: 0.9350 (t) cc_final: 0.8837 (m) REVERT: C 540 LEU cc_start: 0.9252 (tt) cc_final: 0.9020 (tt) REVERT: C 585 MET cc_start: 0.8937 (mmt) cc_final: 0.8274 (mmt) REVERT: C 591 ILE cc_start: 0.8792 (mp) cc_final: 0.8540 (mp) REVERT: C 606 TRP cc_start: 0.8463 (m-10) cc_final: 0.8119 (m-10) REVERT: C 629 MET cc_start: 0.8100 (mtp) cc_final: 0.7679 (tmm) REVERT: C 702 TYR cc_start: 0.8165 (t80) cc_final: 0.7862 (t80) REVERT: C 760 ASP cc_start: 0.8337 (t70) cc_final: 0.8058 (t0) REVERT: C 764 ASN cc_start: 0.8268 (m-40) cc_final: 0.7896 (t0) REVERT: C 1030 ASP cc_start: 0.6659 (p0) cc_final: 0.6353 (m-30) REVERT: C 1062 LEU cc_start: 0.7641 (tp) cc_final: 0.6799 (pt) REVERT: C 1064 ARG cc_start: 0.6868 (mpp80) cc_final: 0.6492 (ttt180) REVERT: C 1153 ILE cc_start: 0.9234 (mt) cc_final: 0.8926 (mm) REVERT: C 1175 TYR cc_start: 0.6765 (m-80) cc_final: 0.6542 (m-80) REVERT: D 580 SER cc_start: 0.8725 (m) cc_final: 0.8371 (m) REVERT: D 625 THR cc_start: 0.8582 (m) cc_final: 0.8152 (p) REVERT: D 714 GLN cc_start: 0.8180 (mm110) cc_final: 0.7596 (mm-40) REVERT: D 752 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8558 (tptt) REVERT: D 1023 MET cc_start: 0.6707 (ttp) cc_final: 0.6399 (ppp) REVERT: D 1101 ARG cc_start: 0.7284 (ppt170) cc_final: 0.6813 (ptm160) REVERT: D 1131 HIS cc_start: 0.6635 (m-70) cc_final: 0.5815 (m-70) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.2771 time to fit residues: 208.2282 Evaluate side-chains 357 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 234 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 30 optimal weight: 0.0010 chunk 108 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 619 ASN A 764 ASN B 791 ASN ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 714 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.096813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.079495 restraints weight = 64902.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081769 restraints weight = 39652.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083261 restraints weight = 27613.982| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19371 Z= 0.220 Angle : 0.692 15.567 26178 Z= 0.365 Chirality : 0.044 0.152 2925 Planarity : 0.005 0.056 3209 Dihedral : 8.031 101.663 2716 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2380 helix: 0.29 (0.14), residues: 1294 sheet: -1.29 (0.40), residues: 163 loop : -2.05 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1177 HIS 0.006 0.002 HIS B1059 PHE 0.023 0.002 PHE B 546 TYR 0.032 0.002 TYR C1031 ARG 0.005 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 918) hydrogen bonds : angle 4.56414 ( 2682) SS BOND : bond 0.00323 ( 12) SS BOND : angle 1.67710 ( 24) covalent geometry : bond 0.00482 (19359) covalent geometry : angle 0.69022 (26154) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 441 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 LEU cc_start: 0.8879 (tp) cc_final: 0.8531 (tp) REVERT: A 808 LEU cc_start: 0.8798 (tp) cc_final: 0.8585 (mm) REVERT: A 1007 VAL cc_start: 0.8707 (t) cc_final: 0.8467 (t) REVERT: A 1025 ILE cc_start: 0.8874 (mm) cc_final: 0.8599 (mt) REVERT: A 1057 MET cc_start: 0.7148 (mpp) cc_final: 0.6584 (mpp) REVERT: A 1191 MET cc_start: 0.7662 (tpt) cc_final: 0.7213 (mmt) REVERT: B 408 MET cc_start: 0.7572 (mmm) cc_final: 0.7363 (mmm) REVERT: B 444 ILE cc_start: 0.8085 (mm) cc_final: 0.7760 (mt) REVERT: B 474 ILE cc_start: 0.9136 (tt) cc_final: 0.8723 (mm) REVERT: B 481 ILE cc_start: 0.7092 (mm) cc_final: 0.6609 (mm) REVERT: B 527 MET cc_start: 0.7267 (ttt) cc_final: 0.6856 (tpp) REVERT: B 591 ILE cc_start: 0.8435 (mt) cc_final: 0.8210 (tt) REVERT: B 642 GLN cc_start: 0.7636 (mt0) cc_final: 0.7393 (tp-100) REVERT: B 697 LYS cc_start: 0.6458 (mmtp) cc_final: 0.6034 (ptmm) REVERT: B 755 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5686 (tp30) REVERT: B 766 TRP cc_start: 0.5872 (t-100) cc_final: 0.5076 (t-100) REVERT: B 768 TYR cc_start: 0.7998 (m-10) cc_final: 0.7527 (m-80) REVERT: B 1005 ARG cc_start: 0.4551 (ptm160) cc_final: 0.4313 (ptm160) REVERT: B 1186 PHE cc_start: 0.7681 (t80) cc_final: 0.7333 (t80) REVERT: C 406 VAL cc_start: 0.9377 (t) cc_final: 0.8850 (m) REVERT: C 424 TYR cc_start: 0.6943 (t80) cc_final: 0.6679 (t80) REVERT: C 585 MET cc_start: 0.8868 (mmt) cc_final: 0.8407 (mmt) REVERT: C 629 MET cc_start: 0.8191 (mtp) cc_final: 0.7737 (tmm) REVERT: C 668 ASP cc_start: 0.9079 (t70) cc_final: 0.8807 (t0) REVERT: C 764 ASN cc_start: 0.8438 (m-40) cc_final: 0.7961 (p0) REVERT: C 1030 ASP cc_start: 0.6893 (p0) cc_final: 0.6239 (m-30) REVERT: C 1064 ARG cc_start: 0.6931 (mpp80) cc_final: 0.6651 (ttt180) REVERT: C 1153 ILE cc_start: 0.9264 (mt) cc_final: 0.8984 (mm) REVERT: C 1175 TYR cc_start: 0.7105 (m-80) cc_final: 0.6756 (m-80) REVERT: D 580 SER cc_start: 0.8679 (m) cc_final: 0.8473 (p) REVERT: D 581 LEU cc_start: 0.8882 (tt) cc_final: 0.8362 (tt) REVERT: D 674 MET cc_start: 0.8084 (mmm) cc_final: 0.7714 (mmt) REVERT: D 1101 ARG cc_start: 0.7252 (ppt170) cc_final: 0.7009 (ptt180) REVERT: D 1131 HIS cc_start: 0.6763 (m-70) cc_final: 0.5840 (m-70) REVERT: D 1134 ILE cc_start: 0.6396 (mp) cc_final: 0.6048 (mm) outliers start: 1 outliers final: 0 residues processed: 442 average time/residue: 0.3020 time to fit residues: 211.9573 Evaluate side-chains 324 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 180 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 791 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS C1148 ASN D 435 HIS D 587 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081000 restraints weight = 64579.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083257 restraints weight = 39458.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.084899 restraints weight = 27446.351| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19371 Z= 0.151 Angle : 0.600 16.010 26178 Z= 0.315 Chirality : 0.041 0.158 2925 Planarity : 0.004 0.058 3209 Dihedral : 7.678 96.687 2716 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2380 helix: 0.62 (0.14), residues: 1306 sheet: -1.26 (0.38), residues: 183 loop : -1.97 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A1177 HIS 0.006 0.001 HIS B1204 PHE 0.026 0.002 PHE B 623 TYR 0.027 0.002 TYR A 711 ARG 0.005 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 918) hydrogen bonds : angle 4.26147 ( 2682) SS BOND : bond 0.00222 ( 12) SS BOND : angle 1.16166 ( 24) covalent geometry : bond 0.00332 (19359) covalent geometry : angle 0.59956 (26154) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 VAL cc_start: 0.9414 (p) cc_final: 0.9176 (p) REVERT: A 730 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8030 (mtpp) REVERT: A 808 LEU cc_start: 0.8759 (tp) cc_final: 0.8542 (mm) REVERT: A 1007 VAL cc_start: 0.8730 (t) cc_final: 0.8520 (t) REVERT: A 1025 ILE cc_start: 0.8846 (mm) cc_final: 0.8570 (mt) REVERT: A 1177 TRP cc_start: 0.5996 (p-90) cc_final: 0.5315 (p-90) REVERT: A 1190 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8216 (mm-30) REVERT: A 1191 MET cc_start: 0.7639 (tpt) cc_final: 0.7119 (mmt) REVERT: B 408 MET cc_start: 0.7672 (mmm) cc_final: 0.7333 (mmm) REVERT: B 444 ILE cc_start: 0.8212 (mm) cc_final: 0.7762 (mt) REVERT: B 474 ILE cc_start: 0.9167 (tt) cc_final: 0.8740 (mm) REVERT: B 481 ILE cc_start: 0.7163 (mm) cc_final: 0.6439 (mm) REVERT: B 524 GLU cc_start: 0.7119 (pm20) cc_final: 0.6903 (pm20) REVERT: B 527 MET cc_start: 0.7234 (ttt) cc_final: 0.6885 (tpp) REVERT: B 591 ILE cc_start: 0.8486 (mt) cc_final: 0.8277 (tt) REVERT: B 697 LYS cc_start: 0.6480 (mmtp) cc_final: 0.5796 (ptmm) REVERT: B 766 TRP cc_start: 0.5808 (t-100) cc_final: 0.5055 (t-100) REVERT: B 768 TYR cc_start: 0.7991 (m-10) cc_final: 0.7445 (m-80) REVERT: C 406 VAL cc_start: 0.9397 (t) cc_final: 0.8907 (m) REVERT: C 424 TYR cc_start: 0.6965 (t80) cc_final: 0.6646 (t80) REVERT: C 590 ASP cc_start: 0.8643 (p0) cc_final: 0.8413 (p0) REVERT: C 629 MET cc_start: 0.8066 (mtp) cc_final: 0.7649 (tmm) REVERT: C 668 ASP cc_start: 0.9087 (t70) cc_final: 0.8800 (t0) REVERT: C 789 LEU cc_start: 0.9116 (mp) cc_final: 0.8783 (mp) REVERT: C 1030 ASP cc_start: 0.6651 (p0) cc_final: 0.6075 (m-30) REVERT: C 1064 ARG cc_start: 0.6748 (mpp80) cc_final: 0.6416 (ttt180) REVERT: C 1141 PHE cc_start: 0.8706 (m-80) cc_final: 0.8385 (m-10) REVERT: C 1153 ILE cc_start: 0.9235 (mt) cc_final: 0.8936 (mm) REVERT: D 549 TYR cc_start: 0.6090 (p90) cc_final: 0.5209 (t80) REVERT: D 580 SER cc_start: 0.8552 (m) cc_final: 0.8275 (p) REVERT: D 1042 LYS cc_start: 0.6824 (pttp) cc_final: 0.6506 (mmtt) REVERT: D 1101 ARG cc_start: 0.7073 (ppt170) cc_final: 0.6710 (ptm160) REVERT: D 1131 HIS cc_start: 0.6684 (m-70) cc_final: 0.5853 (m-70) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.3149 time to fit residues: 217.9696 Evaluate side-chains 336 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 213 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 99 optimal weight: 0.0770 chunk 17 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 791 ASN C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.100293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.083151 restraints weight = 64123.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.085447 restraints weight = 39331.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087115 restraints weight = 27358.618| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19371 Z= 0.112 Angle : 0.562 7.700 26178 Z= 0.293 Chirality : 0.040 0.155 2925 Planarity : 0.004 0.059 3209 Dihedral : 7.247 90.414 2716 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.17), residues: 2380 helix: 0.99 (0.14), residues: 1305 sheet: -0.88 (0.42), residues: 161 loop : -1.86 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1177 HIS 0.005 0.001 HIS D1204 PHE 0.019 0.001 PHE B1186 TYR 0.017 0.001 TYR C1031 ARG 0.003 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 918) hydrogen bonds : angle 4.04652 ( 2682) SS BOND : bond 0.00222 ( 12) SS BOND : angle 0.90242 ( 24) covalent geometry : bond 0.00239 (19359) covalent geometry : angle 0.56175 (26154) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 VAL cc_start: 0.9445 (p) cc_final: 0.9211 (p) REVERT: A 805 LEU cc_start: 0.8949 (tt) cc_final: 0.8726 (tt) REVERT: A 808 LEU cc_start: 0.8709 (tp) cc_final: 0.8498 (mm) REVERT: A 1025 ILE cc_start: 0.8852 (mm) cc_final: 0.8578 (mt) REVERT: A 1177 TRP cc_start: 0.5881 (p-90) cc_final: 0.5528 (p-90) REVERT: A 1190 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8166 (mm-30) REVERT: A 1191 MET cc_start: 0.7666 (tpt) cc_final: 0.7192 (mmt) REVERT: A 1199 MET cc_start: 0.8977 (mtt) cc_final: 0.8635 (mtt) REVERT: B 408 MET cc_start: 0.7577 (mmm) cc_final: 0.7349 (mmm) REVERT: B 444 ILE cc_start: 0.8198 (mm) cc_final: 0.7714 (mt) REVERT: B 474 ILE cc_start: 0.9165 (tt) cc_final: 0.8767 (mm) REVERT: B 481 ILE cc_start: 0.7251 (mm) cc_final: 0.6737 (mm) REVERT: B 498 LEU cc_start: 0.8516 (pt) cc_final: 0.8150 (pt) REVERT: B 527 MET cc_start: 0.7223 (ttt) cc_final: 0.6814 (tpp) REVERT: B 540 LEU cc_start: 0.9191 (tt) cc_final: 0.8972 (tt) REVERT: B 697 LYS cc_start: 0.6354 (mmtp) cc_final: 0.5658 (ptmm) REVERT: B 732 TYR cc_start: 0.7511 (m-10) cc_final: 0.7290 (m-10) REVERT: B 766 TRP cc_start: 0.5726 (t-100) cc_final: 0.5069 (t-100) REVERT: B 768 TYR cc_start: 0.7965 (m-10) cc_final: 0.7466 (m-80) REVERT: C 406 VAL cc_start: 0.9423 (t) cc_final: 0.9167 (t) REVERT: C 424 TYR cc_start: 0.6853 (t80) cc_final: 0.6392 (t80) REVERT: C 590 ASP cc_start: 0.8678 (p0) cc_final: 0.8425 (p0) REVERT: C 606 TRP cc_start: 0.8486 (m-10) cc_final: 0.8211 (m-10) REVERT: C 629 MET cc_start: 0.8034 (mtp) cc_final: 0.7649 (tmm) REVERT: C 714 GLN cc_start: 0.7694 (mm-40) cc_final: 0.6829 (tp40) REVERT: C 764 ASN cc_start: 0.8413 (m110) cc_final: 0.8120 (m110) REVERT: C 789 LEU cc_start: 0.9118 (mp) cc_final: 0.8473 (mp) REVERT: C 1030 ASP cc_start: 0.6505 (p0) cc_final: 0.6118 (m-30) REVERT: C 1064 ARG cc_start: 0.6770 (mpp80) cc_final: 0.6482 (ttt180) REVERT: C 1141 PHE cc_start: 0.8744 (m-80) cc_final: 0.8437 (m-10) REVERT: C 1153 ILE cc_start: 0.9229 (mt) cc_final: 0.8956 (mm) REVERT: D 549 TYR cc_start: 0.6042 (p90) cc_final: 0.5274 (t80) REVERT: D 580 SER cc_start: 0.8643 (m) cc_final: 0.8221 (p) REVERT: D 581 LEU cc_start: 0.8778 (tt) cc_final: 0.8380 (tt) REVERT: D 597 SER cc_start: 0.9295 (p) cc_final: 0.8976 (p) REVERT: D 764 ASN cc_start: 0.8803 (p0) cc_final: 0.8518 (p0) REVERT: D 772 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7268 (mp0) REVERT: D 1042 LYS cc_start: 0.6745 (pttp) cc_final: 0.6540 (mmtm) REVERT: D 1101 ARG cc_start: 0.6935 (ppt170) cc_final: 0.6611 (ptm160) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.3260 time to fit residues: 228.7194 Evaluate side-chains 336 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 97 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 189 optimal weight: 0.2980 chunk 167 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 709 ASN A 756 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 791 ASN ** 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 = 0.3537 r_free = 0.3537 target = 0.097988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080971 restraints weight = 64135.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083233 restraints weight = 39154.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.084846 restraints weight = 27355.086| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19371 Z= 0.170 Angle : 0.627 7.091 26178 Z= 0.327 Chirality : 0.042 0.153 2925 Planarity : 0.004 0.057 3209 Dihedral : 7.350 92.451 2716 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2380 helix: 1.00 (0.14), residues: 1308 sheet: -0.98 (0.43), residues: 152 loop : -1.95 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1177 HIS 0.006 0.001 HIS B1204 PHE 0.022 0.002 PHE B1179 TYR 0.023 0.002 TYR C1031 ARG 0.005 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 918) hydrogen bonds : angle 4.19880 ( 2682) SS BOND : bond 0.00258 ( 12) SS BOND : angle 0.84334 ( 24) covalent geometry : bond 0.00377 (19359) covalent geometry : angle 0.62675 (26154) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 ASN cc_start: 0.7183 (t160) cc_final: 0.6965 (t0) REVERT: A 808 LEU cc_start: 0.8860 (tp) cc_final: 0.8621 (mm) REVERT: A 1025 ILE cc_start: 0.8871 (mm) cc_final: 0.8588 (mt) REVERT: A 1177 TRP cc_start: 0.5955 (p-90) cc_final: 0.5702 (p-90) REVERT: A 1190 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8134 (mm-30) REVERT: A 1191 MET cc_start: 0.7692 (tpt) cc_final: 0.7216 (mmt) REVERT: B 408 MET cc_start: 0.7581 (mmm) cc_final: 0.7262 (mmm) REVERT: B 444 ILE cc_start: 0.8283 (mm) cc_final: 0.7854 (mt) REVERT: B 474 ILE cc_start: 0.9172 (tt) cc_final: 0.8756 (mm) REVERT: B 502 ILE cc_start: 0.7635 (mt) cc_final: 0.7355 (mp) REVERT: B 527 MET cc_start: 0.7192 (ttt) cc_final: 0.6853 (tpp) REVERT: B 540 LEU cc_start: 0.9201 (tt) cc_final: 0.8943 (tt) REVERT: B 697 LYS cc_start: 0.6555 (mmtp) cc_final: 0.6007 (ptmm) REVERT: B 707 THR cc_start: 0.9018 (p) cc_final: 0.8655 (t) REVERT: B 766 TRP cc_start: 0.5902 (t-100) cc_final: 0.5149 (t-100) REVERT: B 768 TYR cc_start: 0.8017 (m-10) cc_final: 0.7446 (m-80) REVERT: C 406 VAL cc_start: 0.9406 (t) cc_final: 0.8924 (m) REVERT: C 424 TYR cc_start: 0.6900 (t80) cc_final: 0.6655 (t80) REVERT: C 585 MET cc_start: 0.9021 (mmt) cc_final: 0.8429 (mmt) REVERT: C 590 ASP cc_start: 0.8684 (p0) cc_final: 0.8413 (p0) REVERT: C 629 MET cc_start: 0.8083 (mtp) cc_final: 0.7628 (tmm) REVERT: C 668 ASP cc_start: 0.9083 (t70) cc_final: 0.8881 (t0) REVERT: C 764 ASN cc_start: 0.8485 (m110) cc_final: 0.8154 (m110) REVERT: C 1030 ASP cc_start: 0.6580 (p0) cc_final: 0.6182 (m-30) REVERT: C 1064 ARG cc_start: 0.6863 (mpp80) cc_final: 0.6543 (ttt180) REVERT: C 1153 ILE cc_start: 0.9266 (mt) cc_final: 0.8997 (mm) REVERT: D 407 MET cc_start: 0.7915 (mmt) cc_final: 0.7629 (mmt) REVERT: D 549 TYR cc_start: 0.6116 (p90) cc_final: 0.5362 (t80) REVERT: D 580 SER cc_start: 0.8522 (m) cc_final: 0.8198 (p) REVERT: D 597 SER cc_start: 0.9337 (p) cc_final: 0.9030 (p) REVERT: D 670 MET cc_start: 0.8425 (mmm) cc_final: 0.8214 (mmt) REVERT: D 674 MET cc_start: 0.8197 (mmm) cc_final: 0.7780 (mmt) REVERT: D 772 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7192 (mp0) REVERT: D 1023 MET cc_start: 0.7196 (ppp) cc_final: 0.6906 (ppp) REVERT: D 1057 MET cc_start: 0.5052 (ttp) cc_final: 0.4675 (ttp) REVERT: D 1131 HIS cc_start: 0.6585 (m90) cc_final: 0.6224 (m90) REVERT: D 1197 VAL cc_start: 0.8816 (t) cc_final: 0.8612 (t) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.2719 time to fit residues: 182.8548 Evaluate side-chains 323 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 108 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 709 ASN B 619 ASN C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083151 restraints weight = 63603.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.085448 restraints weight = 38882.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.087126 restraints weight = 27086.792| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 19371 Z= 0.118 Angle : 0.591 10.658 26178 Z= 0.304 Chirality : 0.041 0.190 2925 Planarity : 0.004 0.058 3209 Dihedral : 7.012 86.276 2716 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2380 helix: 1.17 (0.15), residues: 1304 sheet: -0.95 (0.44), residues: 152 loop : -1.80 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 766 HIS 0.004 0.001 HIS B1204 PHE 0.025 0.001 PHE B1179 TYR 0.021 0.001 TYR A 469 ARG 0.004 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 918) hydrogen bonds : angle 4.01191 ( 2682) SS BOND : bond 0.00315 ( 12) SS BOND : angle 1.13205 ( 24) covalent geometry : bond 0.00261 (19359) covalent geometry : angle 0.59045 (26154) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8433 (t) cc_final: 0.8216 (t) REVERT: A 466 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6919 (mm-30) REVERT: A 469 TYR cc_start: 0.7738 (m-80) cc_final: 0.7513 (m-80) REVERT: A 538 VAL cc_start: 0.9452 (p) cc_final: 0.9160 (p) REVERT: A 730 LYS cc_start: 0.8375 (mttm) cc_final: 0.8137 (mtpp) REVERT: A 808 LEU cc_start: 0.8787 (tp) cc_final: 0.8528 (mm) REVERT: A 1025 ILE cc_start: 0.8863 (mm) cc_final: 0.8571 (mt) REVERT: A 1064 ARG cc_start: 0.6834 (mpp-170) cc_final: 0.6466 (mtp180) REVERT: A 1190 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8193 (mm-30) REVERT: A 1191 MET cc_start: 0.7713 (tpt) cc_final: 0.7251 (mmt) REVERT: B 444 ILE cc_start: 0.8157 (mm) cc_final: 0.7679 (mt) REVERT: B 474 ILE cc_start: 0.9150 (tt) cc_final: 0.8773 (mm) REVERT: B 527 MET cc_start: 0.7211 (ttt) cc_final: 0.6797 (tpp) REVERT: B 540 LEU cc_start: 0.9164 (tt) cc_final: 0.8912 (tt) REVERT: B 581 LEU cc_start: 0.8423 (tp) cc_final: 0.8066 (tp) REVERT: B 585 MET cc_start: 0.8731 (mmm) cc_final: 0.8471 (mmp) REVERT: B 587 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7878 (mm-40) REVERT: B 642 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7081 (pp30) REVERT: B 656 LYS cc_start: 0.7360 (tttt) cc_final: 0.7115 (tttp) REVERT: B 697 LYS cc_start: 0.6457 (mmtp) cc_final: 0.5934 (ptmm) REVERT: B 707 THR cc_start: 0.8995 (p) cc_final: 0.8679 (t) REVERT: B 768 TYR cc_start: 0.7962 (m-10) cc_final: 0.7425 (m-80) REVERT: C 406 VAL cc_start: 0.9418 (t) cc_final: 0.9214 (t) REVERT: C 424 TYR cc_start: 0.6741 (t80) cc_final: 0.6384 (t80) REVERT: C 629 MET cc_start: 0.7958 (mtp) cc_final: 0.7641 (tmm) REVERT: C 674 MET cc_start: 0.8037 (mmt) cc_final: 0.7797 (mmt) REVERT: C 714 GLN cc_start: 0.7706 (mm-40) cc_final: 0.6934 (tp40) REVERT: C 764 ASN cc_start: 0.8368 (m110) cc_final: 0.8033 (m110) REVERT: C 1023 MET cc_start: 0.8430 (mmt) cc_final: 0.8177 (tpp) REVERT: C 1030 ASP cc_start: 0.6427 (p0) cc_final: 0.6206 (m-30) REVERT: C 1064 ARG cc_start: 0.6786 (mpp80) cc_final: 0.6402 (ttt180) REVERT: C 1153 ILE cc_start: 0.9229 (mt) cc_final: 0.8958 (mm) REVERT: D 407 MET cc_start: 0.7846 (mmt) cc_final: 0.7488 (mmt) REVERT: D 549 TYR cc_start: 0.6084 (p90) cc_final: 0.5427 (t80) REVERT: D 580 SER cc_start: 0.8607 (m) cc_final: 0.8282 (p) REVERT: D 607 PHE cc_start: 0.8228 (t80) cc_final: 0.7575 (t80) REVERT: D 674 MET cc_start: 0.8264 (mmm) cc_final: 0.7963 (mmm) REVERT: D 772 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7372 (mp0) REVERT: D 1057 MET cc_start: 0.5113 (ttp) cc_final: 0.4715 (ttp) REVERT: D 1101 ARG cc_start: 0.6888 (ppt170) cc_final: 0.6660 (ptm160) REVERT: D 1131 HIS cc_start: 0.6598 (m90) cc_final: 0.6223 (m90) REVERT: D 1197 VAL cc_start: 0.8805 (t) cc_final: 0.8596 (t) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.3255 time to fit residues: 222.0018 Evaluate side-chains 326 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 179 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 239 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 709 ASN B 619 ASN B1131 HIS ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 791 ASN ** 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 = 0.3539 r_free = 0.3539 target = 0.098200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080906 restraints weight = 64983.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083170 restraints weight = 40117.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.084773 restraints weight = 28174.711| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19371 Z= 0.164 Angle : 0.627 8.240 26178 Z= 0.325 Chirality : 0.042 0.214 2925 Planarity : 0.004 0.055 3209 Dihedral : 7.064 86.739 2716 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2380 helix: 1.16 (0.15), residues: 1307 sheet: -0.93 (0.41), residues: 171 loop : -1.85 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A1177 HIS 0.005 0.001 HIS C 435 PHE 0.024 0.002 PHE B1179 TYR 0.022 0.002 TYR C1031 ARG 0.005 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 918) hydrogen bonds : angle 4.14311 ( 2682) SS BOND : bond 0.00420 ( 12) SS BOND : angle 1.70352 ( 24) covalent geometry : bond 0.00368 (19359) covalent geometry : angle 0.62506 (26154) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8420 (t) cc_final: 0.8190 (t) REVERT: A 466 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7068 (mm-30) REVERT: A 469 TYR cc_start: 0.7803 (m-80) cc_final: 0.7416 (m-10) REVERT: A 808 LEU cc_start: 0.8845 (tp) cc_final: 0.8600 (mm) REVERT: A 1025 ILE cc_start: 0.8833 (mm) cc_final: 0.8541 (mt) REVERT: A 1064 ARG cc_start: 0.6734 (mpp-170) cc_final: 0.6338 (mtp180) REVERT: A 1177 TRP cc_start: 0.6127 (p-90) cc_final: 0.5100 (p-90) REVERT: A 1190 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8124 (mm-30) REVERT: A 1191 MET cc_start: 0.7628 (tpt) cc_final: 0.7170 (mmt) REVERT: B 474 ILE cc_start: 0.9185 (tt) cc_final: 0.8795 (mm) REVERT: B 481 ILE cc_start: 0.7343 (mm) cc_final: 0.6958 (mm) REVERT: B 527 MET cc_start: 0.7290 (ttt) cc_final: 0.6802 (tpp) REVERT: B 540 LEU cc_start: 0.9153 (tt) cc_final: 0.8927 (tt) REVERT: B 642 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7108 (pp30) REVERT: B 697 LYS cc_start: 0.6663 (mmtp) cc_final: 0.6089 (ptmm) REVERT: B 707 THR cc_start: 0.8972 (p) cc_final: 0.8727 (t) REVERT: B 768 TYR cc_start: 0.7995 (m-10) cc_final: 0.7415 (m-80) REVERT: B 1064 ARG cc_start: 0.4598 (mpt180) cc_final: 0.4201 (ppt170) REVERT: C 424 TYR cc_start: 0.6875 (t80) cc_final: 0.6609 (t80) REVERT: C 585 MET cc_start: 0.9030 (mmt) cc_final: 0.8410 (mmt) REVERT: C 590 ASP cc_start: 0.8677 (p0) cc_final: 0.8441 (p0) REVERT: C 629 MET cc_start: 0.8049 (mtp) cc_final: 0.7618 (tmm) REVERT: C 764 ASN cc_start: 0.8479 (m110) cc_final: 0.8134 (m110) REVERT: C 1023 MET cc_start: 0.8449 (mmt) cc_final: 0.8191 (tpp) REVERT: C 1030 ASP cc_start: 0.6477 (p0) cc_final: 0.6117 (m-30) REVERT: C 1064 ARG cc_start: 0.6935 (mpp80) cc_final: 0.6418 (ttt180) REVERT: C 1153 ILE cc_start: 0.9211 (mt) cc_final: 0.8973 (mm) REVERT: D 407 MET cc_start: 0.7914 (mmt) cc_final: 0.7476 (mmt) REVERT: D 549 TYR cc_start: 0.6126 (p90) cc_final: 0.5487 (t80) REVERT: D 580 SER cc_start: 0.8513 (m) cc_final: 0.8214 (p) REVERT: D 597 SER cc_start: 0.9312 (p) cc_final: 0.8976 (p) REVERT: D 670 MET cc_start: 0.8190 (mmt) cc_final: 0.7788 (mmt) REVERT: D 772 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7127 (mp0) REVERT: D 1057 MET cc_start: 0.5079 (ttp) cc_final: 0.4718 (ttp) REVERT: D 1101 ARG cc_start: 0.6968 (ppt170) cc_final: 0.6670 (ptm160) REVERT: D 1116 MET cc_start: 0.7899 (mmm) cc_final: 0.7423 (mpp) REVERT: D 1131 HIS cc_start: 0.6666 (m90) cc_final: 0.6259 (m90) REVERT: D 1197 VAL cc_start: 0.8787 (t) cc_final: 0.8573 (t) outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.2754 time to fit residues: 185.6777 Evaluate side-chains 321 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 60 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 223 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 709 ASN B 619 ASN B 791 ASN ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.096763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079981 restraints weight = 64803.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082243 restraints weight = 39562.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.083670 restraints weight = 27565.549| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19371 Z= 0.195 Angle : 0.667 8.908 26178 Z= 0.348 Chirality : 0.044 0.192 2925 Planarity : 0.004 0.055 3209 Dihedral : 7.331 87.701 2716 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2380 helix: 1.00 (0.15), residues: 1308 sheet: -0.85 (0.45), residues: 140 loop : -1.95 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A1177 HIS 0.004 0.001 HIS D1204 PHE 0.025 0.002 PHE B1179 TYR 0.026 0.002 TYR C1031 ARG 0.006 0.001 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 918) hydrogen bonds : angle 4.30965 ( 2682) SS BOND : bond 0.00466 ( 12) SS BOND : angle 1.51694 ( 24) covalent geometry : bond 0.00435 (19359) covalent geometry : angle 0.66611 (26154) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8464 (t) cc_final: 0.8254 (t) REVERT: A 466 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 469 TYR cc_start: 0.7763 (m-80) cc_final: 0.7524 (m-10) REVERT: A 808 LEU cc_start: 0.8887 (tp) cc_final: 0.8594 (mm) REVERT: A 1025 ILE cc_start: 0.8894 (mm) cc_final: 0.8592 (mt) REVERT: A 1064 ARG cc_start: 0.6709 (mpp-170) cc_final: 0.6241 (mtp180) REVERT: A 1177 TRP cc_start: 0.6158 (p-90) cc_final: 0.4337 (m-10) REVERT: A 1190 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8212 (mm-30) REVERT: A 1191 MET cc_start: 0.7659 (tpt) cc_final: 0.7205 (mmt) REVERT: B 474 ILE cc_start: 0.9189 (tt) cc_final: 0.8792 (mm) REVERT: B 481 ILE cc_start: 0.7324 (mm) cc_final: 0.6816 (mm) REVERT: B 527 MET cc_start: 0.7263 (ttt) cc_final: 0.6938 (tpp) REVERT: B 585 MET cc_start: 0.8800 (mmm) cc_final: 0.8560 (mmp) REVERT: B 642 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7241 (pp30) REVERT: B 697 LYS cc_start: 0.6816 (mmtp) cc_final: 0.6169 (ptmm) REVERT: B 707 THR cc_start: 0.9052 (p) cc_final: 0.8703 (t) REVERT: B 768 TYR cc_start: 0.7988 (m-10) cc_final: 0.7411 (m-80) REVERT: B 1064 ARG cc_start: 0.4606 (mpt180) cc_final: 0.4262 (ppt170) REVERT: B 1181 PHE cc_start: 0.5894 (m-80) cc_final: 0.5631 (m-80) REVERT: B 1201 ILE cc_start: 0.8270 (pt) cc_final: 0.7914 (tp) REVERT: C 406 VAL cc_start: 0.9529 (t) cc_final: 0.9007 (m) REVERT: C 585 MET cc_start: 0.9013 (mmt) cc_final: 0.8497 (mmt) REVERT: C 590 ASP cc_start: 0.8631 (p0) cc_final: 0.8395 (p0) REVERT: C 629 MET cc_start: 0.8027 (mtp) cc_final: 0.7592 (tmm) REVERT: C 637 GLU cc_start: 0.8065 (tp30) cc_final: 0.7684 (tp30) REVERT: C 668 ASP cc_start: 0.9193 (t70) cc_final: 0.8829 (t0) REVERT: C 764 ASN cc_start: 0.8492 (m110) cc_final: 0.8162 (m110) REVERT: C 1023 MET cc_start: 0.8504 (mmt) cc_final: 0.8267 (tpp) REVERT: C 1030 ASP cc_start: 0.6548 (p0) cc_final: 0.6055 (m-30) REVERT: C 1064 ARG cc_start: 0.7157 (mpp80) cc_final: 0.6584 (ttt180) REVERT: C 1153 ILE cc_start: 0.9223 (mt) cc_final: 0.8995 (mm) REVERT: C 1170 LYS cc_start: 0.5951 (mptt) cc_final: 0.5712 (tmmt) REVERT: D 407 MET cc_start: 0.7930 (mmt) cc_final: 0.7258 (mmt) REVERT: D 549 TYR cc_start: 0.6179 (p90) cc_final: 0.5530 (t80) REVERT: D 580 SER cc_start: 0.8467 (m) cc_final: 0.8182 (p) REVERT: D 585 MET cc_start: 0.7885 (mmm) cc_final: 0.7386 (mmm) REVERT: D 597 SER cc_start: 0.9266 (p) cc_final: 0.8950 (p) REVERT: D 674 MET cc_start: 0.8133 (mmm) cc_final: 0.7826 (mmt) REVERT: D 772 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7078 (mp0) REVERT: D 1057 MET cc_start: 0.5127 (ttp) cc_final: 0.4758 (ttp) REVERT: D 1131 HIS cc_start: 0.6952 (m90) cc_final: 0.6571 (m90) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2639 time to fit residues: 169.4891 Evaluate side-chains 315 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 38 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 709 ASN B 791 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS D 586 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.081226 restraints weight = 64463.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083458 restraints weight = 39471.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.085081 restraints weight = 27546.419| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19371 Z= 0.140 Angle : 0.624 7.879 26178 Z= 0.321 Chirality : 0.042 0.206 2925 Planarity : 0.004 0.055 3209 Dihedral : 7.100 86.032 2716 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2380 helix: 1.10 (0.15), residues: 1311 sheet: -0.83 (0.42), residues: 162 loop : -1.91 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A1177 HIS 0.008 0.001 HIS B1204 PHE 0.034 0.002 PHE C1082 TYR 0.021 0.001 TYR C1031 ARG 0.005 0.000 ARG B 453 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 918) hydrogen bonds : angle 4.12628 ( 2682) SS BOND : bond 0.00247 ( 12) SS BOND : angle 1.29368 ( 24) covalent geometry : bond 0.00313 (19359) covalent geometry : angle 0.62279 (26154) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6284.89 seconds wall clock time: 112 minutes 53.15 seconds (6773.15 seconds total)