Starting phenix.real_space_refine on Thu Feb 5 16:59:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnk_26012/02_2026/7tnk_26012.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnk_26012/02_2026/7tnk_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_26012/02_2026/7tnk_26012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnk_26012/02_2026/7tnk_26012.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnk_26012/02_2026/7tnk_26012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnk_26012/02_2026/7tnk_26012.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 4.53, per 1000 atoms: 0.24 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: 1.46 Conformation dependent library (CDL) restraints added in 785.1 milliseconds 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: 0.67 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: 3.39 Time building geometry restraints manager: 1.99 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: 2.060 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.820 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- 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 : 4.80 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG D 628 TYR 0.042 0.003 TYR C1031 PHE 0.038 0.002 PHE C1082 TRP 0.040 0.003 TRP A1177 HIS 0.006 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00523 (19359) covalent geometry : angle 1.01123 (26154) SS BOND : bond 0.00360 ( 12) SS BOND : angle 1.59374 ( 24) hydrogen bonds : bond 0.30382 ( 918) hydrogen bonds : angle 9.77342 ( 2682) *********************** 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 : 0.705 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: 0.7679 (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: 0.8991 (tp) REVERT: A 644 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7612 (mp0) REVERT: A 730 LYS cc_start: 0.8202 (mttt) cc_final: 0.7869 (mmmm) REVERT: A 800 VAL cc_start: 0.9121 (t) cc_final: 0.8893 (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: 0.8863 (mt) REVERT: A 1031 TYR cc_start: 0.6504 (p90) cc_final: 0.5640 (p90) REVERT: A 1155 TYR cc_start: 0.8062 (t80) cc_final: 0.7710 (t80) REVERT: A 1177 TRP cc_start: 0.5743 (p-90) cc_final: 0.4417 (m-10) REVERT: A 1190 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8609 (mm-30) REVERT: A 1191 MET cc_start: 0.7682 (tpt) cc_final: 0.7167 (mmt) REVERT: A 1200 PHE cc_start: 0.8350 (t80) cc_final: 0.7991 (t80) REVERT: A 1205 LYS cc_start: 0.7558 (mtmt) cc_final: 0.6983 (tptp) REVERT: B 399 THR cc_start: 0.8625 (p) cc_final: 0.8386 (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: 0.8451 (tp) REVERT: B 434 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7875 (tttm) REVERT: B 444 ILE cc_start: 0.8093 (mm) cc_final: 0.7539 (mt) REVERT: B 474 ILE cc_start: 0.9096 (tt) cc_final: 0.8762 (mm) REVERT: B 498 LEU cc_start: 0.8975 (pt) cc_final: 0.8655 (pt) REVERT: B 527 MET cc_start: 0.7365 (ttt) cc_final: 0.6909 (tpt) REVERT: B 536 VAL cc_start: 0.8177 (t) cc_final: 0.5900 (p) REVERT: B 586 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7723 (mm-40) REVERT: B 600 ILE cc_start: 0.8871 (mt) cc_final: 0.8587 (mt) REVERT: B 605 TRP cc_start: 0.8307 (t-100) cc_final: 0.7486 (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: 0.4930 (t-100) REVERT: B 800 VAL cc_start: 0.9457 (t) cc_final: 0.9181 (p) REVERT: B 1003 PHE cc_start: 0.3351 (m-10) cc_final: 0.3131 (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: 0.6940 (t80) REVERT: B 1191 MET cc_start: 0.8126 (mtp) cc_final: 0.7622 (mtm) REVERT: C 438 PHE cc_start: 0.7204 (p90) cc_final: 0.5700 (p90) REVERT: C 503 MET cc_start: 0.8424 (ttp) cc_final: 0.7853 (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: 0.7908 (m) REVERT: C 537 SER cc_start: 0.9190 (p) cc_final: 0.8672 (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: 0.7631 (tmm) REVERT: C 702 TYR cc_start: 0.8041 (t80) cc_final: 0.7687 (t80) REVERT: C 764 ASN cc_start: 0.8181 (m-40) cc_final: 0.7873 (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: 0.6425 (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: 0.9204 (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: 0.7739 (mm-30) REVERT: D 434 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8306 (mtpt) REVERT: D 489 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8190 (pp) REVERT: D 503 MET cc_start: 0.8169 (ttm) cc_final: 0.7544 (ptm) REVERT: D 505 LYS cc_start: 0.7491 (ttmt) cc_final: 0.7284 (pptt) REVERT: D 527 MET cc_start: 0.7993 (ptp) cc_final: 0.7691 (mtt) REVERT: D 537 SER cc_start: 0.8796 (p) cc_final: 0.8079 (t) REVERT: D 541 PHE cc_start: 0.8441 (t80) cc_final: 0.8157 (t80) REVERT: D 573 ILE cc_start: 0.9407 (tp) cc_final: 0.9175 (tt) REVERT: D 580 SER cc_start: 0.8574 (m) cc_final: 0.8135 (m) REVERT: D 601 VAL cc_start: 0.9504 (t) cc_final: 0.9298 (p) REVERT: D 629 MET cc_start: 0.5223 (pmt) cc_final: 0.4839 (mmm) REVERT: D 713 GLU cc_start: 0.7875 (tt0) cc_final: 0.7626 (tm-30) REVERT: D 714 GLN cc_start: 0.8376 (mm110) cc_final: 0.7866 (mm110) REVERT: D 752 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8672 (tptt) REVERT: D 1038 VAL cc_start: 0.7192 (t) cc_final: 0.6787 (m) REVERT: D 1062 LEU cc_start: 0.4783 (tp) cc_final: 0.4550 (tp) REVERT: D 1131 HIS cc_start: 0.6296 (m90) cc_final: 0.5990 (m90) REVERT: D 1134 ILE cc_start: 0.6307 (mp) cc_final: 0.6099 (mm) REVERT: D 1204 HIS cc_start: 0.7640 (m170) cc_final: 0.7150 (t-170) REVERT: D 1205 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7487 (mttm) outliers start: 8 outliers final: 0 residues processed: 662 average time/residue: 0.1474 time to fit residues: 147.4828 Evaluate side-chains 399 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN C 586 GLN C 619 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 ** D1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.097006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.079519 restraints weight = 63501.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081688 restraints weight = 39277.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083269 restraints weight = 27747.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084232 restraints weight = 21343.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085035 restraints weight = 17795.067| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 19371 Z= 0.214 Angle : 0.701 7.844 26178 Z= 0.379 Chirality : 0.044 0.236 2925 Planarity : 0.005 0.087 3209 Dihedral : 8.857 105.679 2716 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.25 % Allowed : 3.71 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.15), residues: 2380 helix: -1.10 (0.12), residues: 1288 sheet: -1.72 (0.39), residues: 161 loop : -2.25 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 453 TYR 0.028 0.002 TYR C1031 PHE 0.023 0.002 PHE C 682 TRP 0.026 0.002 TRP A1177 HIS 0.004 0.001 HIS C1198 Details of bonding type rmsd covalent geometry : bond 0.00466 (19359) covalent geometry : angle 0.70022 (26154) SS BOND : bond 0.00863 ( 12) SS BOND : angle 1.40878 ( 24) hydrogen bonds : bond 0.05274 ( 918) hydrogen bonds : angle 5.09402 ( 2682) *********************** 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 491 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 486 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 LEU cc_start: 0.8918 (tp) cc_final: 0.8552 (tp) REVERT: A 573 ILE cc_start: 0.7959 (pt) cc_final: 0.7690 (mt) REVERT: A 808 LEU cc_start: 0.8929 (tp) cc_final: 0.8631 (mm) REVERT: A 1007 VAL cc_start: 0.8774 (t) cc_final: 0.8476 (t) REVERT: A 1020 PHE cc_start: 0.7620 (t80) cc_final: 0.7314 (t80) REVERT: A 1025 ILE cc_start: 0.9093 (mm) cc_final: 0.8879 (mt) REVERT: A 1191 MET cc_start: 0.7623 (tpt) cc_final: 0.7214 (mmt) REVERT: B 399 THR cc_start: 0.8950 (p) cc_final: 0.8682 (t) REVERT: B 408 MET cc_start: 0.7772 (mmm) cc_final: 0.7443 (mmm) REVERT: B 425 CYS cc_start: 0.8634 (m) cc_final: 0.8046 (p) REVERT: B 434 LYS cc_start: 0.8271 (ptpt) cc_final: 0.8018 (tptp) REVERT: B 444 ILE cc_start: 0.8290 (mm) cc_final: 0.7905 (mt) REVERT: B 474 ILE cc_start: 0.9087 (tt) cc_final: 0.8864 (mm) REVERT: B 481 ILE cc_start: 0.7134 (mm) cc_final: 0.6781 (mm) REVERT: B 498 LEU cc_start: 0.8725 (pt) cc_final: 0.8519 (pt) REVERT: B 503 MET cc_start: 0.7104 (ptt) cc_final: 0.6830 (ppp) REVERT: B 527 MET cc_start: 0.7251 (ttt) cc_final: 0.6581 (tpt) REVERT: B 536 VAL cc_start: 0.8619 (t) cc_final: 0.6590 (p) REVERT: B 540 LEU cc_start: 0.9182 (tt) cc_final: 0.8892 (tt) REVERT: B 543 VAL cc_start: 0.8744 (t) cc_final: 0.8515 (p) REVERT: B 586 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8137 (mm-40) REVERT: B 605 TRP cc_start: 0.8282 (t-100) cc_final: 0.7636 (t-100) REVERT: B 697 LYS cc_start: 0.6417 (mmtp) cc_final: 0.5970 (ptmm) REVERT: B 766 TRP cc_start: 0.5821 (t-100) cc_final: 0.5003 (t-100) REVERT: B 1181 PHE cc_start: 0.5881 (m-10) cc_final: 0.5634 (m-80) REVERT: B 1191 MET cc_start: 0.8059 (mtp) cc_final: 0.7217 (tpp) REVERT: C 406 VAL cc_start: 0.9312 (t) cc_final: 0.8712 (m) REVERT: C 585 MET cc_start: 0.8928 (mmt) cc_final: 0.8326 (mmt) REVERT: C 629 MET cc_start: 0.8188 (mtp) cc_final: 0.7634 (tmm) REVERT: C 639 LEU cc_start: 0.8762 (tp) cc_final: 0.8468 (tp) REVERT: C 702 TYR cc_start: 0.8093 (t80) cc_final: 0.7822 (t80) REVERT: C 764 ASN cc_start: 0.8393 (m-40) cc_final: 0.7838 (p0) REVERT: C 1030 ASP cc_start: 0.6820 (p0) cc_final: 0.6290 (m-30) REVERT: C 1062 LEU cc_start: 0.7693 (tp) cc_final: 0.6809 (pt) REVERT: C 1064 ARG cc_start: 0.7068 (mpp80) cc_final: 0.6438 (ttt-90) REVERT: C 1153 ILE cc_start: 0.9288 (mt) cc_final: 0.9005 (mm) REVERT: C 1175 TYR cc_start: 0.6981 (m-80) cc_final: 0.6635 (m-80) REVERT: C 1187 ILE cc_start: 0.9332 (mt) cc_final: 0.9124 (mt) REVERT: C 1195 LEU cc_start: 0.8369 (tt) cc_final: 0.7995 (mm) REVERT: D 509 LYS cc_start: 0.6514 (ptpp) cc_final: 0.5874 (mmpt) REVERT: D 713 GLU cc_start: 0.8371 (tt0) cc_final: 0.8002 (tm-30) REVERT: D 714 GLN cc_start: 0.8493 (mm110) cc_final: 0.7784 (mm-40) REVERT: D 752 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8011 (tptt) REVERT: D 1005 ARG cc_start: 0.6251 (mtp180) cc_final: 0.5185 (ppt170) REVERT: D 1131 HIS cc_start: 0.6473 (m90) cc_final: 0.5644 (m-70) outliers start: 5 outliers final: 0 residues processed: 489 average time/residue: 0.1310 time to fit residues: 100.9793 Evaluate side-chains 354 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 157 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 185 optimal weight: 0.7980 chunk 239 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN B1204 HIS ** 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 D1131 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082404 restraints weight = 63508.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.084755 restraints weight = 38617.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.086418 restraints weight = 26709.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.087336 restraints weight = 20531.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088123 restraints weight = 17245.479| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19371 Z= 0.125 Angle : 0.603 13.848 26178 Z= 0.316 Chirality : 0.040 0.153 2925 Planarity : 0.004 0.077 3209 Dihedral : 8.023 98.679 2716 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.10 % Allowed : 3.07 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2380 helix: -0.07 (0.14), residues: 1287 sheet: -1.53 (0.40), residues: 155 loop : -2.04 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1098 TYR 0.024 0.001 TYR A 711 PHE 0.015 0.001 PHE C1082 TRP 0.038 0.001 TRP A1177 HIS 0.004 0.001 HIS B1059 Details of bonding type rmsd covalent geometry : bond 0.00262 (19359) covalent geometry : angle 0.60186 (26154) SS BOND : bond 0.00334 ( 12) SS BOND : angle 1.21716 ( 24) hydrogen bonds : bond 0.04285 ( 918) hydrogen bonds : angle 4.44270 ( 2682) *********************** 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 469 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 467 time to evaluate : 0.735 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 405 TYR cc_start: 0.8149 (m-80) cc_final: 0.7897 (m-80) REVERT: A 538 VAL cc_start: 0.9353 (p) cc_final: 0.9091 (p) REVERT: A 728 ASP cc_start: 0.8172 (p0) cc_final: 0.7701 (p0) REVERT: A 730 LYS cc_start: 0.8317 (mttm) cc_final: 0.8055 (mttt) REVERT: A 764 ASN cc_start: 0.8526 (m-40) cc_final: 0.8275 (m110) REVERT: A 808 LEU cc_start: 0.8754 (tp) cc_final: 0.8526 (mm) REVERT: A 1025 ILE cc_start: 0.8900 (mm) cc_final: 0.8616 (mt) REVERT: A 1032 TRP cc_start: 0.7379 (m100) cc_final: 0.6267 (m100) REVERT: A 1177 TRP cc_start: 0.6169 (p-90) cc_final: 0.5843 (p-90) REVERT: A 1190 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8284 (mm-30) REVERT: A 1191 MET cc_start: 0.7713 (tpt) cc_final: 0.7216 (mmt) REVERT: B 399 THR cc_start: 0.8848 (p) cc_final: 0.8511 (t) REVERT: B 408 MET cc_start: 0.7651 (mmm) cc_final: 0.7361 (mmm) REVERT: B 434 LYS cc_start: 0.8182 (ptpt) cc_final: 0.7975 (tttm) REVERT: B 444 ILE cc_start: 0.8224 (mm) cc_final: 0.7847 (mt) REVERT: B 474 ILE cc_start: 0.9092 (tt) cc_final: 0.8855 (mm) REVERT: B 527 MET cc_start: 0.7402 (ttt) cc_final: 0.6345 (tpt) REVERT: B 540 LEU cc_start: 0.9256 (tt) cc_final: 0.8898 (tt) REVERT: B 697 LYS cc_start: 0.6286 (mmtp) cc_final: 0.5606 (ptmm) REVERT: B 699 LYS cc_start: 0.7602 (tttm) cc_final: 0.7285 (mmpt) REVERT: B 766 TRP cc_start: 0.5722 (t-100) cc_final: 0.4995 (t-100) REVERT: B 768 TYR cc_start: 0.8005 (m-10) cc_final: 0.7503 (m-80) REVERT: B 1191 MET cc_start: 0.7812 (mtp) cc_final: 0.7198 (tpp) REVERT: C 406 VAL cc_start: 0.9329 (t) cc_final: 0.8855 (m) REVERT: C 424 TYR cc_start: 0.6921 (t80) cc_final: 0.6495 (t80) REVERT: C 540 LEU cc_start: 0.9295 (tt) cc_final: 0.9085 (tt) REVERT: C 606 TRP cc_start: 0.8407 (m-10) cc_final: 0.8053 (m-10) REVERT: C 629 MET cc_start: 0.8028 (mtp) cc_final: 0.7594 (tmm) REVERT: C 702 TYR cc_start: 0.8027 (t80) cc_final: 0.7807 (t80) REVERT: C 764 ASN cc_start: 0.8207 (m-40) cc_final: 0.7841 (t0) REVERT: C 1030 ASP cc_start: 0.6607 (p0) cc_final: 0.6210 (m-30) REVERT: C 1062 LEU cc_start: 0.7689 (tp) cc_final: 0.6892 (pt) REVERT: C 1064 ARG cc_start: 0.6737 (mpp80) cc_final: 0.6475 (ttt180) REVERT: C 1153 ILE cc_start: 0.9255 (mt) cc_final: 0.8945 (mm) REVERT: C 1175 TYR cc_start: 0.6711 (m-80) cc_final: 0.6396 (m-80) REVERT: C 1195 LEU cc_start: 0.8420 (tt) cc_final: 0.8155 (mm) REVERT: D 463 MET cc_start: 0.6887 (ttp) cc_final: 0.6685 (ttm) REVERT: D 479 LEU cc_start: 0.8871 (mt) cc_final: 0.8489 (mt) REVERT: D 580 SER cc_start: 0.8628 (m) cc_final: 0.8197 (m) REVERT: D 625 THR cc_start: 0.8594 (m) cc_final: 0.8156 (p) REVERT: D 714 GLN cc_start: 0.8336 (mm110) cc_final: 0.7465 (mm-40) REVERT: D 752 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8642 (tptt) REVERT: D 1005 ARG cc_start: 0.6020 (mtp180) cc_final: 0.5388 (ppt170) REVERT: D 1023 MET cc_start: 0.6676 (ttp) cc_final: 0.6467 (ppp) REVERT: D 1109 LEU cc_start: 0.8274 (tp) cc_final: 0.8020 (tp) REVERT: D 1131 HIS cc_start: 0.6545 (m-70) cc_final: 0.6215 (m90) outliers start: 2 outliers final: 0 residues processed: 468 average time/residue: 0.1332 time to fit residues: 98.4986 Evaluate side-chains 350 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 112 optimal weight: 9.9990 chunk 201 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 217 optimal weight: 20.0000 chunk 136 optimal weight: 0.0870 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.097812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.080516 restraints weight = 65227.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082644 restraints weight = 40755.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.084197 restraints weight = 28907.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.085165 restraints weight = 22490.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085893 restraints weight = 18862.624| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19371 Z= 0.181 Angle : 0.632 13.456 26178 Z= 0.334 Chirality : 0.042 0.156 2925 Planarity : 0.004 0.066 3209 Dihedral : 7.886 101.303 2716 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.17), residues: 2380 helix: 0.30 (0.14), residues: 1296 sheet: -1.29 (0.39), residues: 173 loop : -2.02 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.026 0.002 TYR C1031 PHE 0.023 0.002 PHE B1181 TRP 0.025 0.002 TRP A1177 HIS 0.008 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00399 (19359) covalent geometry : angle 0.63208 (26154) SS BOND : bond 0.00458 ( 12) SS BOND : angle 0.97965 ( 24) hydrogen bonds : bond 0.04108 ( 918) hydrogen bonds : angle 4.37991 ( 2682) *********************** 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 444 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.777 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 466 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6992 (mm-30) REVERT: A 483 LEU cc_start: 0.8834 (tp) cc_final: 0.8501 (tp) REVERT: A 538 VAL cc_start: 0.9416 (p) cc_final: 0.9203 (p) REVERT: A 764 ASN cc_start: 0.8550 (m-40) cc_final: 0.8294 (m110) REVERT: A 808 LEU cc_start: 0.8754 (tp) cc_final: 0.8545 (mm) REVERT: A 1025 ILE cc_start: 0.8861 (mm) cc_final: 0.8588 (mt) REVERT: A 1177 TRP cc_start: 0.5932 (p-90) cc_final: 0.5613 (p-90) REVERT: A 1190 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8265 (mm-30) REVERT: A 1191 MET cc_start: 0.7660 (tpt) cc_final: 0.7168 (mmt) REVERT: B 399 THR cc_start: 0.8974 (p) cc_final: 0.8598 (t) REVERT: B 408 MET cc_start: 0.7574 (mmm) cc_final: 0.7293 (mmm) REVERT: B 434 LYS cc_start: 0.8218 (ptpt) cc_final: 0.7963 (tttm) REVERT: B 444 ILE cc_start: 0.8344 (mm) cc_final: 0.7941 (mt) REVERT: B 474 ILE cc_start: 0.9178 (tt) cc_final: 0.8725 (mm) REVERT: B 481 ILE cc_start: 0.7259 (mm) cc_final: 0.6746 (mm) REVERT: B 527 MET cc_start: 0.7192 (ttt) cc_final: 0.6853 (tpp) REVERT: B 540 LEU cc_start: 0.9214 (tt) cc_final: 0.8954 (tt) REVERT: B 697 LYS cc_start: 0.6426 (mmtp) cc_final: 0.5905 (ptmm) REVERT: B 707 THR cc_start: 0.8955 (p) cc_final: 0.8584 (t) REVERT: B 766 TRP cc_start: 0.5868 (t-100) cc_final: 0.5088 (t-100) REVERT: B 768 TYR cc_start: 0.7952 (m-10) cc_final: 0.7418 (m-80) REVERT: B 1181 PHE cc_start: 0.6100 (m-10) cc_final: 0.5876 (m-80) REVERT: B 1186 PHE cc_start: 0.7731 (t80) cc_final: 0.7461 (t80) REVERT: B 1191 MET cc_start: 0.7756 (mtp) cc_final: 0.7235 (tpp) REVERT: B 1202 ASP cc_start: 0.8810 (m-30) cc_final: 0.8575 (m-30) REVERT: C 406 VAL cc_start: 0.9366 (t) cc_final: 0.8826 (m) REVERT: C 424 TYR cc_start: 0.7019 (t80) cc_final: 0.6698 (t80) REVERT: C 503 MET cc_start: 0.8376 (ptt) cc_final: 0.8132 (ppp) REVERT: C 585 MET cc_start: 0.8924 (mmt) cc_final: 0.8390 (mmt) REVERT: C 629 MET cc_start: 0.8099 (mtp) cc_final: 0.7665 (tmm) REVERT: C 668 ASP cc_start: 0.9021 (t70) cc_final: 0.8773 (t0) REVERT: C 1030 ASP cc_start: 0.6683 (p0) cc_final: 0.6124 (m-30) REVERT: C 1062 LEU cc_start: 0.7669 (tp) cc_final: 0.6888 (pt) REVERT: C 1064 ARG cc_start: 0.6801 (mpp80) cc_final: 0.6567 (ttt180) REVERT: C 1153 ILE cc_start: 0.9218 (mt) cc_final: 0.8898 (mm) REVERT: C 1175 TYR cc_start: 0.6869 (m-80) cc_final: 0.6527 (m-80) REVERT: C 1195 LEU cc_start: 0.8499 (tt) cc_final: 0.8245 (mm) REVERT: D 479 LEU cc_start: 0.8714 (mt) cc_final: 0.8482 (mt) REVERT: D 580 SER cc_start: 0.8629 (m) cc_final: 0.8354 (m) REVERT: D 581 LEU cc_start: 0.8810 (tt) cc_final: 0.8412 (tt) REVERT: D 597 SER cc_start: 0.9327 (p) cc_final: 0.9051 (p) REVERT: D 752 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8137 (tptt) REVERT: D 1131 HIS cc_start: 0.6635 (m-70) cc_final: 0.5788 (m-70) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.1281 time to fit residues: 90.5598 Evaluate side-chains 341 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 19 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN C 619 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.099693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082519 restraints weight = 64394.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.084818 restraints weight = 39493.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086385 restraints weight = 27561.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.087556 restraints weight = 21150.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088242 restraints weight = 17460.832| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19371 Z= 0.118 Angle : 0.575 14.971 26178 Z= 0.299 Chirality : 0.040 0.156 2925 Planarity : 0.004 0.057 3209 Dihedral : 7.445 92.729 2716 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.05 % Allowed : 2.33 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2380 helix: 0.67 (0.14), residues: 1304 sheet: -1.31 (0.38), residues: 177 loop : -1.91 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 453 TYR 0.025 0.001 TYR A 711 PHE 0.024 0.001 PHE B 623 TRP 0.023 0.001 TRP A1177 HIS 0.005 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00251 (19359) covalent geometry : angle 0.57414 (26154) SS BOND : bond 0.00416 ( 12) SS BOND : angle 0.98040 ( 24) hydrogen bonds : bond 0.03724 ( 918) hydrogen bonds : angle 4.07633 ( 2682) *********************** 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 460 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 VAL cc_start: 0.9429 (p) cc_final: 0.9197 (p) REVERT: A 728 ASP cc_start: 0.8318 (p0) cc_final: 0.7995 (t70) REVERT: A 764 ASN cc_start: 0.8555 (m-40) cc_final: 0.8240 (m110) REVERT: A 808 LEU cc_start: 0.8690 (tp) cc_final: 0.8464 (mm) REVERT: A 1025 ILE cc_start: 0.8852 (mm) cc_final: 0.8562 (mt) REVERT: A 1032 TRP cc_start: 0.7422 (m100) cc_final: 0.6457 (m100) REVERT: A 1190 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8192 (mm-30) REVERT: A 1191 MET cc_start: 0.7640 (tpt) cc_final: 0.7225 (mmt) REVERT: B 406 VAL cc_start: 0.7288 (t) cc_final: 0.6941 (p) REVERT: B 408 MET cc_start: 0.7538 (mmm) cc_final: 0.7331 (mmm) REVERT: B 444 ILE cc_start: 0.8433 (mm) cc_final: 0.8072 (mt) REVERT: B 474 ILE cc_start: 0.9145 (tt) cc_final: 0.8734 (mm) REVERT: B 481 ILE cc_start: 0.7223 (mm) cc_final: 0.6673 (mm) REVERT: B 527 MET cc_start: 0.7110 (ttt) cc_final: 0.6806 (tpp) REVERT: B 540 LEU cc_start: 0.9160 (tt) cc_final: 0.8900 (tt) REVERT: B 697 LYS cc_start: 0.6379 (mmtp) cc_final: 0.5903 (ptmm) REVERT: B 707 THR cc_start: 0.8950 (p) cc_final: 0.8570 (t) REVERT: B 766 TRP cc_start: 0.5764 (t-100) cc_final: 0.5086 (t-100) REVERT: B 768 TYR cc_start: 0.7981 (m-10) cc_final: 0.7515 (m-80) REVERT: B 1181 PHE cc_start: 0.5995 (m-10) cc_final: 0.5777 (m-80) REVERT: B 1186 PHE cc_start: 0.7738 (t80) cc_final: 0.7375 (t80) REVERT: B 1191 MET cc_start: 0.7699 (mtp) cc_final: 0.7261 (tpp) REVERT: C 406 VAL cc_start: 0.9373 (t) cc_final: 0.8849 (m) REVERT: C 424 TYR cc_start: 0.6964 (t80) cc_final: 0.6553 (t80) REVERT: C 629 MET cc_start: 0.7950 (mtp) cc_final: 0.7610 (tmm) REVERT: C 668 ASP cc_start: 0.9033 (t70) cc_final: 0.8789 (t0) REVERT: C 764 ASN cc_start: 0.8357 (m110) cc_final: 0.8034 (m110) REVERT: C 1030 ASP cc_start: 0.6472 (p0) cc_final: 0.6065 (m-30) REVERT: C 1062 LEU cc_start: 0.7575 (tp) cc_final: 0.6890 (pt) REVERT: C 1064 ARG cc_start: 0.6694 (mpp80) cc_final: 0.6460 (ttt180) REVERT: C 1141 PHE cc_start: 0.8775 (m-80) cc_final: 0.8436 (m-80) REVERT: C 1153 ILE cc_start: 0.9165 (mt) cc_final: 0.8860 (mm) REVERT: C 1195 LEU cc_start: 0.8493 (tt) cc_final: 0.8206 (mm) REVERT: D 405 TYR cc_start: 0.7792 (m-80) cc_final: 0.7543 (m-80) REVERT: D 549 TYR cc_start: 0.5957 (p90) cc_final: 0.5170 (t80) REVERT: D 580 SER cc_start: 0.8562 (m) cc_final: 0.8272 (p) REVERT: D 629 MET cc_start: 0.4627 (tpt) cc_final: 0.4366 (mmm) REVERT: D 713 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7621 (tm-30) REVERT: D 752 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8027 (tptt) REVERT: D 772 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7355 (mp0) REVERT: D 1042 LYS cc_start: 0.6716 (pttp) cc_final: 0.6471 (mmtt) REVERT: D 1131 HIS cc_start: 0.6624 (m-70) cc_final: 0.6265 (m90) REVERT: D 1197 VAL cc_start: 0.8800 (t) cc_final: 0.8597 (t) outliers start: 1 outliers final: 0 residues processed: 460 average time/residue: 0.1065 time to fit residues: 79.6168 Evaluate side-chains 342 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 222 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 204 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 139 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN C 586 GLN C 619 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D1204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083518 restraints weight = 63261.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.085823 restraints weight = 38790.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087447 restraints weight = 27123.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.088620 restraints weight = 20764.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089261 restraints weight = 17030.489| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19371 Z= 0.112 Angle : 0.575 13.122 26178 Z= 0.294 Chirality : 0.041 0.294 2925 Planarity : 0.004 0.057 3209 Dihedral : 7.133 88.893 2716 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2380 helix: 0.95 (0.14), residues: 1303 sheet: -1.01 (0.42), residues: 157 loop : -1.84 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 453 TYR 0.016 0.001 TYR C1031 PHE 0.041 0.001 PHE D1020 TRP 0.050 0.001 TRP A1177 HIS 0.005 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00239 (19359) covalent geometry : angle 0.57354 (26154) SS BOND : bond 0.00222 ( 12) SS BOND : angle 1.23743 ( 24) hydrogen bonds : bond 0.03555 ( 918) hydrogen bonds : angle 3.98697 ( 2682) *********************** 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 463 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 VAL cc_start: 0.9432 (p) cc_final: 0.9191 (p) REVERT: A 728 ASP cc_start: 0.8197 (p0) cc_final: 0.7898 (t70) REVERT: A 764 ASN cc_start: 0.8564 (m-40) cc_final: 0.8263 (m110) REVERT: A 808 LEU cc_start: 0.8735 (tp) cc_final: 0.8496 (mm) REVERT: A 1025 ILE cc_start: 0.8841 (mm) cc_final: 0.8559 (mt) REVERT: A 1032 TRP cc_start: 0.7188 (m100) cc_final: 0.6003 (m100) REVERT: A 1177 TRP cc_start: 0.6156 (p-90) cc_final: 0.5429 (p-90) REVERT: A 1190 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8183 (mm-30) REVERT: A 1191 MET cc_start: 0.7710 (tpt) cc_final: 0.7191 (mmt) REVERT: A 1195 LEU cc_start: 0.8476 (mt) cc_final: 0.7941 (mt) REVERT: A 1199 MET cc_start: 0.8889 (mtt) cc_final: 0.8610 (mtt) REVERT: B 408 MET cc_start: 0.7544 (mmm) cc_final: 0.7328 (mmm) REVERT: B 444 ILE cc_start: 0.8096 (mm) cc_final: 0.7646 (mt) REVERT: B 474 ILE cc_start: 0.9085 (tt) cc_final: 0.8668 (mm) REVERT: B 540 LEU cc_start: 0.9195 (tt) cc_final: 0.8952 (tt) REVERT: B 656 LYS cc_start: 0.7447 (tttt) cc_final: 0.7078 (tttt) REVERT: B 682 PHE cc_start: 0.5186 (m-10) cc_final: 0.4662 (m-10) REVERT: B 697 LYS cc_start: 0.6384 (mmtp) cc_final: 0.5975 (ptmm) REVERT: B 707 THR cc_start: 0.8965 (p) cc_final: 0.8582 (t) REVERT: B 766 TRP cc_start: 0.5737 (t-100) cc_final: 0.5088 (t-100) REVERT: B 768 TYR cc_start: 0.7976 (m-10) cc_final: 0.7516 (m-80) REVERT: B 1181 PHE cc_start: 0.6021 (m-10) cc_final: 0.5733 (m-80) REVERT: C 406 VAL cc_start: 0.9373 (t) cc_final: 0.9108 (t) REVERT: C 424 TYR cc_start: 0.6902 (t80) cc_final: 0.6358 (t80) REVERT: C 425 CYS cc_start: 0.8715 (m) cc_final: 0.8483 (m) REVERT: C 503 MET cc_start: 0.8504 (ppp) cc_final: 0.8011 (ppp) REVERT: C 585 MET cc_start: 0.8895 (mmt) cc_final: 0.8351 (mmt) REVERT: C 606 TRP cc_start: 0.8410 (m-10) cc_final: 0.8182 (m-10) REVERT: C 629 MET cc_start: 0.7941 (mtp) cc_final: 0.7626 (tmm) REVERT: C 1030 ASP cc_start: 0.6516 (p0) cc_final: 0.6183 (m-30) REVERT: C 1062 LEU cc_start: 0.7519 (tp) cc_final: 0.6854 (pt) REVERT: C 1064 ARG cc_start: 0.6677 (mpp80) cc_final: 0.6437 (ttt180) REVERT: C 1153 ILE cc_start: 0.9152 (mt) cc_final: 0.8849 (mm) REVERT: C 1195 LEU cc_start: 0.8586 (tt) cc_final: 0.8290 (mm) REVERT: D 405 TYR cc_start: 0.7497 (m-80) cc_final: 0.7207 (m-80) REVERT: D 549 TYR cc_start: 0.5872 (p90) cc_final: 0.5221 (t80) REVERT: D 580 SER cc_start: 0.8646 (m) cc_final: 0.8219 (p) REVERT: D 581 LEU cc_start: 0.8754 (tt) cc_final: 0.8374 (tt) REVERT: D 625 THR cc_start: 0.8601 (m) cc_final: 0.8121 (p) REVERT: D 633 ILE cc_start: 0.7050 (pt) cc_final: 0.6660 (tt) REVERT: D 713 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7591 (tm-30) REVERT: D 752 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8559 (tptt) REVERT: D 1131 HIS cc_start: 0.6535 (m-70) cc_final: 0.6152 (m90) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.1136 time to fit residues: 84.2089 Evaluate side-chains 354 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 199 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 212 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 98 optimal weight: 0.0010 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 619 ASN B1131 HIS C 619 ASN C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D1206 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.101211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083943 restraints weight = 63999.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.086216 restraints weight = 39506.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087448 restraints weight = 27760.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.088759 restraints weight = 22336.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.089440 restraints weight = 18393.000| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19371 Z= 0.106 Angle : 0.565 9.675 26178 Z= 0.288 Chirality : 0.040 0.270 2925 Planarity : 0.004 0.056 3209 Dihedral : 6.773 86.211 2716 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.05 % Allowed : 1.78 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2380 helix: 1.14 (0.14), residues: 1305 sheet: -0.91 (0.42), residues: 156 loop : -1.82 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 453 TYR 0.016 0.001 TYR C1031 PHE 0.022 0.001 PHE D1020 TRP 0.032 0.001 TRP A1177 HIS 0.005 0.001 HIS D1204 Details of bonding type rmsd covalent geometry : bond 0.00231 (19359) covalent geometry : angle 0.56440 (26154) SS BOND : bond 0.00169 ( 12) SS BOND : angle 0.87016 ( 24) hydrogen bonds : bond 0.03397 ( 918) hydrogen bonds : angle 3.91442 ( 2682) *********************** 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 458 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 457 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 VAL cc_start: 0.9441 (p) cc_final: 0.9181 (p) REVERT: A 585 MET cc_start: 0.7619 (mmm) cc_final: 0.7289 (mmm) REVERT: A 764 ASN cc_start: 0.8569 (m-40) cc_final: 0.8076 (m110) REVERT: A 808 LEU cc_start: 0.8714 (tp) cc_final: 0.8460 (mm) REVERT: A 1025 ILE cc_start: 0.8777 (mm) cc_final: 0.8471 (mt) REVERT: A 1032 TRP cc_start: 0.7294 (m100) cc_final: 0.6046 (m100) REVERT: A 1064 ARG cc_start: 0.6978 (mpp-170) cc_final: 0.6554 (mtp180) REVERT: A 1177 TRP cc_start: 0.5946 (p-90) cc_final: 0.5734 (p-90) REVERT: A 1190 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8160 (mm-30) REVERT: A 1191 MET cc_start: 0.7770 (tpt) cc_final: 0.7262 (mmt) REVERT: A 1195 LEU cc_start: 0.8517 (mt) cc_final: 0.8211 (mt) REVERT: B 444 ILE cc_start: 0.8075 (mm) cc_final: 0.7635 (mt) REVERT: B 474 ILE cc_start: 0.9104 (tt) cc_final: 0.8711 (mm) REVERT: B 481 ILE cc_start: 0.7144 (mm) cc_final: 0.6803 (mm) REVERT: B 517 PHE cc_start: 0.8435 (p90) cc_final: 0.8220 (p90) REVERT: B 540 LEU cc_start: 0.9187 (tt) cc_final: 0.8924 (tt) REVERT: B 585 MET cc_start: 0.8812 (mmm) cc_final: 0.8550 (mmp) REVERT: B 613 ILE cc_start: 0.9181 (mm) cc_final: 0.8873 (mm) REVERT: B 656 LYS cc_start: 0.7418 (tttt) cc_final: 0.7045 (mtpt) REVERT: B 697 LYS cc_start: 0.6348 (mmtp) cc_final: 0.5688 (ptmm) REVERT: B 707 THR cc_start: 0.8945 (p) cc_final: 0.8585 (t) REVERT: B 755 GLU cc_start: 0.6601 (pp20) cc_final: 0.5669 (tm-30) REVERT: B 766 TRP cc_start: 0.5718 (t-100) cc_final: 0.5046 (t-100) REVERT: B 768 TYR cc_start: 0.7963 (m-10) cc_final: 0.7498 (m-80) REVERT: C 406 VAL cc_start: 0.9359 (t) cc_final: 0.9149 (t) REVERT: C 424 TYR cc_start: 0.6766 (t80) cc_final: 0.6344 (t80) REVERT: C 503 MET cc_start: 0.8420 (ppp) cc_final: 0.8102 (ppp) REVERT: C 585 MET cc_start: 0.8565 (mmt) cc_final: 0.8136 (mmt) REVERT: C 629 MET cc_start: 0.7939 (mtp) cc_final: 0.7660 (tmm) REVERT: C 668 ASP cc_start: 0.9042 (t70) cc_final: 0.8818 (t0) REVERT: C 708 MET cc_start: 0.7959 (mmm) cc_final: 0.7751 (mmm) REVERT: C 1030 ASP cc_start: 0.6505 (p0) cc_final: 0.6242 (m-30) REVERT: C 1062 LEU cc_start: 0.7511 (tp) cc_final: 0.6856 (pt) REVERT: C 1064 ARG cc_start: 0.6701 (mpp80) cc_final: 0.6451 (ttt180) REVERT: C 1175 TYR cc_start: 0.6492 (m-80) cc_final: 0.6262 (m-80) REVERT: C 1191 MET cc_start: 0.6941 (mmm) cc_final: 0.6559 (mmm) REVERT: C 1195 LEU cc_start: 0.8588 (tt) cc_final: 0.8241 (mm) REVERT: D 549 TYR cc_start: 0.5845 (p90) cc_final: 0.5270 (t80) REVERT: D 580 SER cc_start: 0.8479 (m) cc_final: 0.8176 (p) REVERT: D 625 THR cc_start: 0.8588 (m) cc_final: 0.8084 (p) REVERT: D 629 MET cc_start: 0.4765 (tpt) cc_final: 0.4506 (mmm) REVERT: D 674 MET cc_start: 0.8057 (mmm) cc_final: 0.7798 (mmm) REVERT: D 713 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7546 (tm-30) REVERT: D 752 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8532 (tptt) REVERT: D 1057 MET cc_start: 0.5278 (ttp) cc_final: 0.4970 (ttp) outliers start: 1 outliers final: 0 residues processed: 457 average time/residue: 0.1023 time to fit residues: 76.5235 Evaluate side-chains 348 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 203 optimal weight: 0.1980 chunk 179 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B1131 HIS ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN C 619 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082150 restraints weight = 64350.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.084398 restraints weight = 39868.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085900 restraints weight = 28067.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087089 restraints weight = 21786.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.087741 restraints weight = 18040.752| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19371 Z= 0.148 Angle : 0.629 10.347 26178 Z= 0.322 Chirality : 0.042 0.283 2925 Planarity : 0.004 0.065 3209 Dihedral : 6.715 85.967 2716 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2380 helix: 1.07 (0.14), residues: 1306 sheet: -0.99 (0.39), residues: 172 loop : -1.96 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.021 0.001 TYR C1031 PHE 0.040 0.002 PHE B 546 TRP 0.030 0.001 TRP A1177 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd covalent geometry : bond 0.00332 (19359) covalent geometry : angle 0.62687 (26154) SS BOND : bond 0.00237 ( 12) SS BOND : angle 1.95619 ( 24) hydrogen bonds : bond 0.03594 ( 918) hydrogen bonds : angle 4.09426 ( 2682) *********************** 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 434 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.761 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: 0.8499 (t) cc_final: 0.8293 (t) REVERT: A 538 VAL cc_start: 0.9429 (p) cc_final: 0.9227 (p) REVERT: A 764 ASN cc_start: 0.8610 (m-40) cc_final: 0.8291 (m110) REVERT: A 808 LEU cc_start: 0.8806 (tp) cc_final: 0.8520 (mm) REVERT: A 1025 ILE cc_start: 0.8861 (mm) cc_final: 0.8559 (mt) REVERT: A 1064 ARG cc_start: 0.6946 (mpp-170) cc_final: 0.6515 (mtp180) REVERT: A 1177 TRP cc_start: 0.6242 (p-90) cc_final: 0.5693 (p-90) REVERT: A 1190 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8209 (mm-30) REVERT: A 1191 MET cc_start: 0.7705 (tpt) cc_final: 0.7207 (mmt) REVERT: B 444 ILE cc_start: 0.8185 (mm) cc_final: 0.7769 (mt) REVERT: B 474 ILE cc_start: 0.9080 (tt) cc_final: 0.8672 (mm) REVERT: B 540 LEU cc_start: 0.9225 (tt) cc_final: 0.8934 (tt) REVERT: B 656 LYS cc_start: 0.7500 (tttt) cc_final: 0.7131 (mtpt) REVERT: B 697 LYS cc_start: 0.6458 (mmtp) cc_final: 0.5767 (ptmm) REVERT: B 707 THR cc_start: 0.8988 (p) cc_final: 0.8651 (t) REVERT: B 755 GLU cc_start: 0.6784 (pp20) cc_final: 0.5997 (tp30) REVERT: B 766 TRP cc_start: 0.5817 (t-100) cc_final: 0.5097 (t-100) REVERT: B 768 TYR cc_start: 0.7977 (m-10) cc_final: 0.7529 (m-80) REVERT: C 424 TYR cc_start: 0.6770 (t80) cc_final: 0.6386 (t80) REVERT: C 503 MET cc_start: 0.8448 (ppp) cc_final: 0.8104 (ppp) REVERT: C 585 MET cc_start: 0.8955 (mmt) cc_final: 0.8416 (mmt) REVERT: C 629 MET cc_start: 0.8024 (mtp) cc_final: 0.7690 (tmm) REVERT: C 643 THR cc_start: 0.7187 (p) cc_final: 0.6977 (p) REVERT: C 668 ASP cc_start: 0.9078 (t70) cc_final: 0.8858 (t0) REVERT: C 1030 ASP cc_start: 0.6456 (p0) cc_final: 0.6104 (m-30) REVERT: C 1062 LEU cc_start: 0.7499 (tp) cc_final: 0.6807 (pt) REVERT: C 1064 ARG cc_start: 0.6744 (mpp80) cc_final: 0.6523 (ttt180) REVERT: C 1153 ILE cc_start: 0.9193 (mt) cc_final: 0.8934 (mm) REVERT: C 1175 TYR cc_start: 0.6556 (m-80) cc_final: 0.6313 (m-80) REVERT: C 1191 MET cc_start: 0.7020 (mmm) cc_final: 0.6710 (mmm) REVERT: C 1195 LEU cc_start: 0.8564 (tt) cc_final: 0.8204 (mm) REVERT: D 549 TYR cc_start: 0.5969 (p90) cc_final: 0.5387 (t80) REVERT: D 580 SER cc_start: 0.8563 (m) cc_final: 0.8198 (p) REVERT: D 597 SER cc_start: 0.9285 (p) cc_final: 0.8919 (p) REVERT: D 629 MET cc_start: 0.4729 (tpt) cc_final: 0.4419 (mmm) REVERT: D 674 MET cc_start: 0.8078 (mmm) cc_final: 0.7833 (mmm) REVERT: D 752 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8483 (tptt) REVERT: D 1023 MET cc_start: 0.7049 (ppp) cc_final: 0.6784 (ppp) REVERT: D 1057 MET cc_start: 0.5217 (ttp) cc_final: 0.4878 (ttp) REVERT: D 1197 VAL cc_start: 0.8807 (t) cc_final: 0.8599 (t) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.1033 time to fit residues: 74.0088 Evaluate side-chains 335 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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: 5.9990 chunk 231 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 165 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 709 ASN A 764 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS D 435 HIS ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.080004 restraints weight = 64997.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.082082 restraints weight = 40747.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083580 restraints weight = 29103.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084591 restraints weight = 22682.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.085370 restraints weight = 18974.604| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19371 Z= 0.207 Angle : 0.688 8.582 26178 Z= 0.358 Chirality : 0.044 0.269 2925 Planarity : 0.004 0.053 3209 Dihedral : 6.991 89.630 2716 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2380 helix: 0.89 (0.14), residues: 1304 sheet: -1.26 (0.39), residues: 173 loop : -2.00 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 453 TYR 0.027 0.002 TYR C1031 PHE 0.027 0.002 PHE C1181 TRP 0.027 0.002 TRP A1177 HIS 0.005 0.001 HIS C1081 Details of bonding type rmsd covalent geometry : bond 0.00460 (19359) covalent geometry : angle 0.68677 (26154) SS BOND : bond 0.00338 ( 12) SS BOND : angle 1.62592 ( 24) hydrogen bonds : bond 0.03958 ( 918) hydrogen bonds : angle 4.38013 ( 2682) *********************** 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 416 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8480 (t) cc_final: 0.8256 (t) REVERT: A 483 LEU cc_start: 0.8766 (tp) cc_final: 0.8476 (tp) REVERT: A 619 ASN cc_start: 0.6808 (t160) cc_final: 0.6578 (t0) REVERT: A 764 ASN cc_start: 0.8529 (m110) cc_final: 0.8271 (m110) REVERT: A 808 LEU cc_start: 0.8904 (tp) cc_final: 0.8606 (mm) REVERT: A 1025 ILE cc_start: 0.8878 (mm) cc_final: 0.8561 (mt) REVERT: A 1064 ARG cc_start: 0.7043 (mpp-170) cc_final: 0.6552 (mtp180) REVERT: A 1190 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8396 (mm-30) REVERT: A 1191 MET cc_start: 0.7607 (tpt) cc_final: 0.7145 (mmt) REVERT: B 444 ILE cc_start: 0.8248 (mm) cc_final: 0.7894 (mt) REVERT: B 474 ILE cc_start: 0.9135 (tt) cc_final: 0.8705 (mm) REVERT: B 585 MET cc_start: 0.8779 (mmm) cc_final: 0.8527 (mmp) REVERT: B 697 LYS cc_start: 0.6672 (mmtp) cc_final: 0.6094 (ptmm) REVERT: B 707 THR cc_start: 0.9059 (p) cc_final: 0.8689 (t) REVERT: B 755 GLU cc_start: 0.6827 (pp20) cc_final: 0.6140 (tp30) REVERT: B 766 TRP cc_start: 0.5883 (t-100) cc_final: 0.5079 (t-100) REVERT: B 768 TYR cc_start: 0.7977 (m-10) cc_final: 0.7447 (m-80) REVERT: C 424 TYR cc_start: 0.6917 (t80) cc_final: 0.6628 (t80) REVERT: C 503 MET cc_start: 0.8491 (ppp) cc_final: 0.8095 (ppp) REVERT: C 585 MET cc_start: 0.8893 (mmt) cc_final: 0.8400 (mmt) REVERT: C 629 MET cc_start: 0.8060 (mtp) cc_final: 0.7602 (tmm) REVERT: C 668 ASP cc_start: 0.9115 (t70) cc_final: 0.8798 (t0) REVERT: C 764 ASN cc_start: 0.8424 (m110) cc_final: 0.7868 (t0) REVERT: C 1030 ASP cc_start: 0.6631 (p0) cc_final: 0.6084 (m-30) REVERT: C 1064 ARG cc_start: 0.6965 (mpp80) cc_final: 0.6616 (ttt180) REVERT: C 1153 ILE cc_start: 0.9235 (mt) cc_final: 0.8978 (mm) REVERT: C 1175 TYR cc_start: 0.6638 (m-80) cc_final: 0.6223 (m-80) REVERT: C 1195 LEU cc_start: 0.8594 (tt) cc_final: 0.8228 (mm) REVERT: D 549 TYR cc_start: 0.6031 (p90) cc_final: 0.5451 (t80) REVERT: D 581 LEU cc_start: 0.8859 (tt) cc_final: 0.8377 (tt) REVERT: D 629 MET cc_start: 0.4797 (tpt) cc_final: 0.4579 (mmm) REVERT: D 674 MET cc_start: 0.8091 (mmm) cc_final: 0.7849 (mmm) REVERT: D 752 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8517 (tptt) REVERT: D 772 GLU cc_start: 0.5999 (mp0) cc_final: 0.5552 (mm-30) REVERT: D 1057 MET cc_start: 0.5138 (ttp) cc_final: 0.4820 (ttp) REVERT: D 1116 MET cc_start: 0.8042 (mmm) cc_final: 0.7479 (mpp) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.1120 time to fit residues: 76.4139 Evaluate side-chains 319 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 176 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 217 optimal weight: 0.1980 chunk 181 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 709 ASN B 619 ASN C 586 GLN C 619 ASN C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 642 GLN ** D1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.081416 restraints weight = 64178.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083666 restraints weight = 39183.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.085294 restraints weight = 27227.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.086293 restraints weight = 20897.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087111 restraints weight = 17347.810| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19371 Z= 0.151 Angle : 0.635 8.866 26178 Z= 0.327 Chirality : 0.043 0.291 2925 Planarity : 0.004 0.053 3209 Dihedral : 6.753 87.088 2716 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2380 helix: 1.02 (0.14), residues: 1302 sheet: -1.17 (0.40), residues: 170 loop : -1.97 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 453 TYR 0.023 0.001 TYR C1031 PHE 0.033 0.002 PHE C1082 TRP 0.026 0.001 TRP A1177 HIS 0.008 0.001 HIS D1204 Details of bonding type rmsd covalent geometry : bond 0.00336 (19359) covalent geometry : angle 0.63359 (26154) SS BOND : bond 0.00345 ( 12) SS BOND : angle 1.35309 ( 24) hydrogen bonds : bond 0.03688 ( 918) hydrogen bonds : angle 4.20763 ( 2682) ********************** 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 414 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.718 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: 0.8503 (t) cc_final: 0.8279 (t) REVERT: A 585 MET cc_start: 0.7645 (mmm) cc_final: 0.7444 (mmm) REVERT: A 764 ASN cc_start: 0.8465 (m110) cc_final: 0.8248 (m110) REVERT: A 808 LEU cc_start: 0.8872 (tp) cc_final: 0.8586 (mm) REVERT: A 1025 ILE cc_start: 0.8866 (mm) cc_final: 0.8565 (mt) REVERT: A 1064 ARG cc_start: 0.6980 (mpp-170) cc_final: 0.6522 (mtp180) REVERT: A 1177 TRP cc_start: 0.6029 (p-90) cc_final: 0.5674 (p-90) REVERT: A 1190 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 1191 MET cc_start: 0.7649 (tpt) cc_final: 0.7158 (mmt) REVERT: A 1195 LEU cc_start: 0.8485 (mt) cc_final: 0.8274 (mt) REVERT: B 444 ILE cc_start: 0.8185 (mm) cc_final: 0.7800 (mt) REVERT: B 474 ILE cc_start: 0.9114 (tt) cc_final: 0.8692 (mm) REVERT: B 581 LEU cc_start: 0.8375 (tp) cc_final: 0.8173 (tp) REVERT: B 656 LYS cc_start: 0.7541 (tttt) cc_final: 0.7050 (tttt) REVERT: B 697 LYS cc_start: 0.6662 (mmtp) cc_final: 0.6056 (ptmm) REVERT: B 707 THR cc_start: 0.9017 (p) cc_final: 0.8670 (t) REVERT: B 755 GLU cc_start: 0.6866 (pp20) cc_final: 0.6139 (tp30) REVERT: B 766 TRP cc_start: 0.5786 (t-100) cc_final: 0.5071 (t-100) REVERT: B 768 TYR cc_start: 0.7997 (m-10) cc_final: 0.7437 (m-80) REVERT: C 424 TYR cc_start: 0.6899 (t80) cc_final: 0.6439 (t80) REVERT: C 503 MET cc_start: 0.8462 (ppp) cc_final: 0.8065 (ppp) REVERT: C 585 MET cc_start: 0.9010 (mmt) cc_final: 0.8510 (mmt) REVERT: C 629 MET cc_start: 0.7978 (mtp) cc_final: 0.7554 (tmm) REVERT: C 668 ASP cc_start: 0.9104 (t70) cc_final: 0.8899 (t0) REVERT: C 764 ASN cc_start: 0.8351 (m110) cc_final: 0.7842 (t0) REVERT: C 1030 ASP cc_start: 0.6359 (p0) cc_final: 0.6022 (m-30) REVERT: C 1064 ARG cc_start: 0.7015 (mpp80) cc_final: 0.6533 (ttt180) REVERT: C 1153 ILE cc_start: 0.9214 (mt) cc_final: 0.8969 (mm) REVERT: C 1175 TYR cc_start: 0.6558 (m-80) cc_final: 0.6222 (m-80) REVERT: C 1191 MET cc_start: 0.7064 (mmm) cc_final: 0.6699 (mmm) REVERT: C 1195 LEU cc_start: 0.8568 (tt) cc_final: 0.8236 (mm) REVERT: D 629 MET cc_start: 0.4949 (tpt) cc_final: 0.4717 (mmm) REVERT: D 674 MET cc_start: 0.8131 (mmm) cc_final: 0.7889 (mmm) REVERT: D 752 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8518 (tptt) REVERT: D 772 GLU cc_start: 0.5972 (mp0) cc_final: 0.5518 (mm-30) REVERT: D 1057 MET cc_start: 0.5214 (ttp) cc_final: 0.4882 (ttp) REVERT: D 1197 VAL cc_start: 0.8843 (t) cc_final: 0.8642 (t) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1060 time to fit residues: 70.9084 Evaluate side-chains 322 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 0 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 211 optimal weight: 0.0270 chunk 207 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 190 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 overall best weight: 1.7842 ------------------------------------------------------------------------------- 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 709 ASN B 619 ASN ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C1131 HIS C1148 ASN C1204 HIS D 435 HIS D 586 GLN D 642 GLN ** D1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081467 restraints weight = 64379.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083724 restraints weight = 39232.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.085342 restraints weight = 27243.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086314 restraints weight = 20854.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087117 restraints weight = 17340.034| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19371 Z= 0.148 Angle : 0.641 8.849 26178 Z= 0.328 Chirality : 0.042 0.220 2925 Planarity : 0.004 0.054 3209 Dihedral : 6.624 86.168 2716 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2380 helix: 1.07 (0.14), residues: 1308 sheet: -1.21 (0.41), residues: 164 loop : -1.96 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 453 TYR 0.022 0.001 TYR C1031 PHE 0.039 0.002 PHE B 546 TRP 0.023 0.001 TRP A1177 HIS 0.009 0.001 HIS D1204 Details of bonding type rmsd covalent geometry : bond 0.00332 (19359) covalent geometry : angle 0.64068 (26154) SS BOND : bond 0.00286 ( 12) SS BOND : angle 1.20763 ( 24) hydrogen bonds : bond 0.03638 ( 918) hydrogen bonds : angle 4.17363 ( 2682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2853.71 seconds wall clock time: 50 minutes 22.35 seconds (3022.35 seconds total)