Starting phenix.real_space_refine on Sat Sep 12 23:07:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tnk_26012/09_2026/7tnk_26012.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnk_26012/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tnk_26012/09_2026/7tnk_26012.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tnk_26012/09_2026/7tnk_26012.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tnk_26012/09_2026/7tnk_26012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnk_26012/09_2026/7tnk_26012.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnk_26012/09_2026/7tnk_26012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnk_26012/09_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-2.2.1-6174/lib/python3.11/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: 4.19, per 1000 atoms: 0.22 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: 1.67 Conformation dependent library (CDL) restraints added in 832.8 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: 0.58 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: 3.61 Time building geometry restraints manager: 2.24 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 - 20.63: 10893 20.63 - 41.26: 423 41.26 - 61.89: 28 61.89 - 82.52: 5 82.52 - 103.15: 4 Dihedral angle restraints: 11353 sinusoidal: 4426 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 11350 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.100 Find NCS groups from input model: 0.490 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 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 : 11.050 103.155 6901 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/Z covalent geometry : bond 0.00523 / 0.25 (19359) covalent geometry : angle 1.01123 / 0.57 (26154) SS BOND : bond 0.00360 / 0.18 ( 12) SS BOND : angle 1.59374 / 1.05 ( 24) hydrogen bonds : bond 0.30382 / 20.34 ( 918) hydrogen bonds : angle 9.77342 / 6.76 ( 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 : 0.727 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: 0.1423 time to fit residues: 143.6791 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 : 0.719 ------------------------------------------------------------------------------- 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... 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 = 0.3521 r_free = 0.3521 target = 0.096951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079450 restraints weight = 63466.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081691 restraints weight = 39228.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083182 restraints weight = 27477.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084241 restraints weight = 21235.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085060 restraints weight = 17629.600| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 19371 Z= 0.211 Angle : 0.695 7.737 26178 Z= 0.376 Chirality : 0.043 0.152 2925 Planarity : 0.005 0.087 3209 Dihedral : 6.832 93.963 2620 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.20 % Allowed : 3.56 % Favored : 96.24 % 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: -2.50 (0.15), residues: 2380 helix: -1.14 (0.12), residues: 1283 sheet: -1.72 (0.39), residues: 161 loop : -2.24 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 453 TYR 0.028 0.002 TYR C1031 PHE 0.022 0.002 PHE C 682 TRP 0.027 0.002 TRP A1177 HIS 0.004 0.001 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (19359) covalent geometry : angle 0.69386 / 0.38 (26154) SS BOND : bond 0.00975 / 0.65 ( 12) SS BOND : angle 1.58900 / 1.22 ( 24) hydrogen bonds : bond 0.05468 / 3.64 ( 918) hydrogen bonds : angle 5.10611 / 3.56 ( 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 488 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 484 time to evaluate : 0.733 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: 0.8916 (tp) cc_final: 0.8569 (tp) REVERT: A 573 ILE cc_start: 0.7951 (pt) cc_final: 0.7677 (mt) REVERT: A 808 LEU cc_start: 0.8917 (tp) cc_final: 0.8628 (mm) REVERT: A 1007 VAL cc_start: 0.8774 (t) cc_final: 0.8477 (t) REVERT: A 1020 PHE cc_start: 0.7622 (t80) cc_final: 0.7329 (t80) REVERT: A 1025 ILE cc_start: 0.9084 (mm) cc_final: 0.8866 (mt) REVERT: A 1191 MET cc_start: 0.7624 (tpt) cc_final: 0.7207 (mmt) REVERT: B 399 THR cc_start: 0.8951 (p) cc_final: 0.8590 (t) REVERT: B 408 MET cc_start: 0.7779 (mmm) cc_final: 0.7438 (mmm) REVERT: B 425 CYS cc_start: 0.8633 (m) cc_final: 0.8041 (p) REVERT: B 434 LYS cc_start: 0.8277 (ptpt) cc_final: 0.8057 (tttm) REVERT: B 444 ILE cc_start: 0.8290 (mm) cc_final: 0.7894 (mt) REVERT: B 474 ILE cc_start: 0.9086 (tt) cc_final: 0.8852 (mm) REVERT: B 481 ILE cc_start: 0.7135 (mm) cc_final: 0.6790 (mm) REVERT: B 498 LEU cc_start: 0.8728 (pt) cc_final: 0.8516 (pt) REVERT: B 503 MET cc_start: 0.7009 (ptt) cc_final: 0.6773 (ppp) REVERT: B 527 MET cc_start: 0.7253 (ttt) cc_final: 0.6529 (tpt) REVERT: B 536 VAL cc_start: 0.8619 (t) cc_final: 0.6598 (p) REVERT: B 540 LEU cc_start: 0.9180 (tt) cc_final: 0.8893 (tt) REVERT: B 543 VAL cc_start: 0.8741 (t) cc_final: 0.8509 (p) REVERT: B 586 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8139 (mm-40) REVERT: B 605 TRP cc_start: 0.8278 (t-100) cc_final: 0.7644 (t-100) REVERT: B 697 LYS cc_start: 0.6411 (mmtp) cc_final: 0.5972 (ptmm) REVERT: B 766 TRP cc_start: 0.5826 (t-100) cc_final: 0.5008 (t-100) REVERT: B 1181 PHE cc_start: 0.5880 (m-10) cc_final: 0.5610 (m-80) REVERT: B 1191 MET cc_start: 0.8056 (mtp) cc_final: 0.7212 (tpp) REVERT: C 406 VAL cc_start: 0.9316 (t) cc_final: 0.8714 (m) REVERT: C 503 MET cc_start: 0.8204 (ttp) cc_final: 0.7871 (ppp) REVERT: C 585 MET cc_start: 0.8931 (mmt) cc_final: 0.8320 (mmt) REVERT: C 629 MET cc_start: 0.8190 (mtp) cc_final: 0.7651 (tmm) REVERT: C 639 LEU cc_start: 0.8760 (tp) cc_final: 0.8469 (tp) REVERT: C 702 TYR cc_start: 0.8076 (t80) cc_final: 0.7774 (t80) REVERT: C 764 ASN cc_start: 0.8397 (m-40) cc_final: 0.7842 (p0) REVERT: C 1030 ASP cc_start: 0.6815 (p0) cc_final: 0.6272 (m-30) REVERT: C 1062 LEU cc_start: 0.7691 (tp) cc_final: 0.6801 (pt) REVERT: C 1064 ARG cc_start: 0.7083 (mpp80) cc_final: 0.6450 (ttt-90) REVERT: C 1153 ILE cc_start: 0.9288 (mt) cc_final: 0.9003 (mm) REVERT: C 1175 TYR cc_start: 0.6993 (m-80) cc_final: 0.6657 (m-80) REVERT: C 1195 LEU cc_start: 0.8381 (tt) cc_final: 0.8007 (mm) REVERT: D 509 LYS cc_start: 0.6508 (ptpp) cc_final: 0.5884 (mmpt) REVERT: D 713 GLU cc_start: 0.8355 (tt0) cc_final: 0.7976 (tm-30) REVERT: D 714 GLN cc_start: 0.8497 (mm110) cc_final: 0.7755 (mm-40) REVERT: D 752 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8045 (tptt) REVERT: D 1005 ARG cc_start: 0.6251 (mtp180) cc_final: 0.5161 (ppt170) REVERT: D 1101 ARG cc_start: 0.7177 (ppt170) cc_final: 0.6725 (ptm160) REVERT: D 1131 HIS cc_start: 0.6476 (m90) cc_final: 0.5643 (m-70) outliers start: 4 outliers final: 0 residues processed: 487 average time/residue: 0.1285 time to fit residues: 99.2422 Evaluate side-chains 352 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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: 0.0470 chunk 160 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3557 r_free = 0.3557 target = 0.099222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.082177 restraints weight = 62988.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084427 restraints weight = 38067.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.086083 restraints weight = 26579.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087001 restraints weight = 20343.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087830 restraints weight = 16986.918| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3897 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= 0.127 Angle : 0.593 11.839 26178 Z= 0.315 Chirality : 0.041 0.154 2925 Planarity : 0.004 0.076 3209 Dihedral : 6.160 88.645 2620 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.63 % 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: 1286 sheet: -1.55 (0.40), residues: 160 loop : -2.03 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1098 TYR 0.019 0.001 TYR C1031 PHE 0.020 0.001 PHE B1179 TRP 0.040 0.001 TRP A1177 HIS 0.004 0.001 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (19359) covalent geometry : angle 0.59194 / 0.31 (26154) SS BOND : bond 0.00484 / 0.25 ( 12) SS BOND : angle 1.20611 / 0.76 ( 24) hydrogen bonds : bond 0.04280 / 2.83 ( 918) hydrogen bonds : angle 4.42730 / 3.10 ( 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: 1 poor density : 468 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 TYR cc_start: 0.8160 (m-80) cc_final: 0.7915 (m-80) REVERT: A 469 TYR cc_start: 0.7690 (m-10) cc_final: 0.7462 (m-80) REVERT: A 538 VAL cc_start: 0.9354 (p) cc_final: 0.9074 (p) REVERT: A 764 ASN cc_start: 0.8539 (m-40) cc_final: 0.8307 (m110) REVERT: A 808 LEU cc_start: 0.8759 (tp) cc_final: 0.8535 (mm) REVERT: A 1007 VAL cc_start: 0.8786 (t) cc_final: 0.8483 (t) REVERT: A 1025 ILE cc_start: 0.8941 (mm) cc_final: 0.8668 (mt) REVERT: A 1032 TRP cc_start: 0.7423 (m100) cc_final: 0.6324 (m100) REVERT: A 1063 TRP cc_start: 0.7368 (m-90) cc_final: 0.7125 (m-10) REVERT: A 1177 TRP cc_start: 0.6133 (p-90) cc_final: 0.5853 (p-90) REVERT: A 1190 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8281 (mm-30) REVERT: A 1191 MET cc_start: 0.7643 (tpt) cc_final: 0.7176 (mmt) REVERT: B 399 THR cc_start: 0.8948 (p) cc_final: 0.8589 (t) REVERT: B 408 MET cc_start: 0.7657 (mmm) cc_final: 0.7367 (mmm) REVERT: B 434 LYS cc_start: 0.8195 (ptpt) cc_final: 0.7986 (tttm) REVERT: B 444 ILE cc_start: 0.8237 (mm) cc_final: 0.7782 (mt) REVERT: B 474 ILE cc_start: 0.9106 (tt) cc_final: 0.8861 (mm) REVERT: B 481 ILE cc_start: 0.7166 (mm) cc_final: 0.6658 (mm) REVERT: B 527 MET cc_start: 0.7397 (ttt) cc_final: 0.6295 (tpt) REVERT: B 540 LEU cc_start: 0.9266 (tt) cc_final: 0.8906 (tt) REVERT: B 697 LYS cc_start: 0.6289 (mmtp) cc_final: 0.5618 (ptmm) REVERT: B 699 LYS cc_start: 0.7576 (tttm) cc_final: 0.7246 (mmpt) REVERT: B 768 TYR cc_start: 0.8036 (m-10) cc_final: 0.7548 (m-80) REVERT: B 1191 MET cc_start: 0.7827 (mtp) cc_final: 0.7191 (tpp) REVERT: C 406 VAL cc_start: 0.9326 (t) cc_final: 0.8841 (m) REVERT: C 424 TYR cc_start: 0.6941 (t80) cc_final: 0.6537 (t80) REVERT: C 540 LEU cc_start: 0.9309 (tt) cc_final: 0.9102 (tt) REVERT: C 606 TRP cc_start: 0.8438 (m-10) cc_final: 0.8114 (m-10) REVERT: C 629 MET cc_start: 0.8028 (mtp) cc_final: 0.7585 (tmm) REVERT: C 702 TYR cc_start: 0.8075 (t80) cc_final: 0.7775 (t80) REVERT: C 764 ASN cc_start: 0.8280 (m-40) cc_final: 0.7903 (t0) REVERT: C 1030 ASP cc_start: 0.6598 (p0) cc_final: 0.6196 (m-30) REVERT: C 1057 MET cc_start: 0.8269 (mtm) cc_final: 0.7984 (mtp) REVERT: C 1062 LEU cc_start: 0.7670 (tp) cc_final: 0.6890 (pt) REVERT: C 1064 ARG cc_start: 0.6711 (mpp80) cc_final: 0.6459 (ttt180) REVERT: C 1153 ILE cc_start: 0.9235 (mt) cc_final: 0.8936 (mm) REVERT: C 1175 TYR cc_start: 0.6723 (m-80) cc_final: 0.6385 (m-80) REVERT: C 1195 LEU cc_start: 0.8423 (tt) cc_final: 0.8136 (mm) REVERT: D 479 LEU cc_start: 0.8876 (mt) cc_final: 0.8520 (mt) REVERT: D 580 SER cc_start: 0.8686 (m) cc_final: 0.8249 (m) REVERT: D 581 LEU cc_start: 0.8756 (tt) cc_final: 0.8541 (tt) REVERT: D 713 GLU cc_start: 0.8270 (tt0) cc_final: 0.8048 (tm-30) REVERT: D 714 GLN cc_start: 0.8311 (mm110) cc_final: 0.7460 (mm-40) REVERT: D 752 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8004 (tptt) REVERT: D 1005 ARG cc_start: 0.6039 (mtp180) cc_final: 0.5364 (ppt170) REVERT: D 1023 MET cc_start: 0.6747 (ttp) cc_final: 0.6490 (ppp) REVERT: D 1109 LEU cc_start: 0.8319 (tp) cc_final: 0.8069 (tp) REVERT: D 1131 HIS cc_start: 0.6510 (m-70) cc_final: 0.6164 (m90) outliers start: 1 outliers final: 0 residues processed: 468 average time/residue: 0.1328 time to fit residues: 99.2084 Evaluate side-chains 353 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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: 2.9990 chunk 177 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 217 optimal weight: 0.0980 chunk 136 optimal weight: 6.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.080470 restraints weight = 64821.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082707 restraints weight = 39601.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.084168 restraints weight = 27619.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.085379 restraints weight = 21362.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.086134 restraints weight = 17487.391| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19371 Z= 0.179 Angle : 0.627 12.858 26178 Z= 0.333 Chirality : 0.042 0.159 2925 Planarity : 0.004 0.063 3209 Dihedral : 6.097 89.765 2620 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: -1.04 (0.17), residues: 2380 helix: 0.29 (0.14), residues: 1295 sheet: -1.30 (0.39), residues: 174 loop : -1.97 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.025 0.002 TYR C1031 PHE 0.021 0.002 PHE B1181 TRP 0.025 0.002 TRP A1177 HIS 0.008 0.001 HIS B1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (19359) covalent geometry : angle 0.62695 / 0.33 (26154) SS BOND : bond 0.00226 / 0.15 ( 12) SS BOND : angle 1.03918 / 0.65 ( 24) hydrogen bonds : bond 0.04149 / 2.73 ( 918) hydrogen bonds : angle 4.38738 / 3.06 ( 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 442 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.745 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: 0.7183 (mm-30) cc_final: 0.6947 (mm-30) REVERT: A 469 TYR cc_start: 0.7801 (m-10) cc_final: 0.7564 (m-80) REVERT: A 538 VAL cc_start: 0.9405 (p) cc_final: 0.9169 (p) REVERT: A 764 ASN cc_start: 0.8567 (m-40) cc_final: 0.8287 (m110) REVERT: A 1007 VAL cc_start: 0.8730 (t) cc_final: 0.8466 (t) REVERT: A 1025 ILE cc_start: 0.8863 (mm) cc_final: 0.8582 (mt) REVERT: A 1063 TRP cc_start: 0.7476 (m-90) cc_final: 0.7235 (m-10) REVERT: A 1177 TRP cc_start: 0.5939 (p-90) cc_final: 0.5621 (p-90) REVERT: A 1190 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8218 (mm-30) REVERT: A 1191 MET cc_start: 0.7653 (tpt) cc_final: 0.7152 (mmt) REVERT: B 406 VAL cc_start: 0.7325 (t) cc_final: 0.7056 (p) REVERT: B 408 MET cc_start: 0.7566 (mmm) cc_final: 0.7340 (mmm) REVERT: B 434 LYS cc_start: 0.8182 (ptpt) cc_final: 0.7971 (tttm) REVERT: B 444 ILE cc_start: 0.8329 (mm) cc_final: 0.8000 (mt) REVERT: B 474 ILE cc_start: 0.9158 (tt) cc_final: 0.8729 (mm) REVERT: B 527 MET cc_start: 0.7199 (ttt) cc_final: 0.6774 (tpp) REVERT: B 540 LEU cc_start: 0.9206 (tt) cc_final: 0.8967 (tt) REVERT: B 697 LYS cc_start: 0.6481 (mmtp) cc_final: 0.5950 (ptmm) REVERT: B 766 TRP cc_start: 0.5775 (t-100) cc_final: 0.5330 (t-100) REVERT: B 768 TYR cc_start: 0.7935 (m-10) cc_final: 0.7437 (m-80) REVERT: B 1181 PHE cc_start: 0.6132 (m-10) cc_final: 0.5920 (m-80) REVERT: B 1186 PHE cc_start: 0.7659 (t80) cc_final: 0.7439 (t80) REVERT: B 1191 MET cc_start: 0.7750 (mtp) cc_final: 0.7213 (tpp) REVERT: B 1202 ASP cc_start: 0.8811 (m-30) cc_final: 0.8575 (m-30) REVERT: C 406 VAL cc_start: 0.9374 (t) cc_final: 0.8802 (m) REVERT: C 424 TYR cc_start: 0.6987 (t80) cc_final: 0.6698 (t80) REVERT: C 503 MET cc_start: 0.8417 (ptt) cc_final: 0.8138 (ppp) REVERT: C 585 MET cc_start: 0.8941 (mmt) cc_final: 0.8392 (mmt) REVERT: C 629 MET cc_start: 0.8120 (mtp) cc_final: 0.7658 (tmm) REVERT: C 668 ASP cc_start: 0.9018 (t70) cc_final: 0.8764 (t0) REVERT: C 1030 ASP cc_start: 0.6676 (p0) cc_final: 0.6122 (m-30) REVERT: C 1062 LEU cc_start: 0.7610 (tp) cc_final: 0.6889 (pt) REVERT: C 1064 ARG cc_start: 0.6785 (mpp80) cc_final: 0.6543 (ttt180) REVERT: C 1153 ILE cc_start: 0.9217 (mt) cc_final: 0.8895 (mm) REVERT: C 1175 TYR cc_start: 0.6833 (m-80) cc_final: 0.6505 (m-80) REVERT: C 1195 LEU cc_start: 0.8513 (tt) cc_final: 0.8243 (mm) REVERT: D 479 LEU cc_start: 0.8658 (mt) cc_final: 0.8286 (mt) REVERT: D 580 SER cc_start: 0.8573 (m) cc_final: 0.8348 (m) REVERT: D 597 SER cc_start: 0.9306 (p) cc_final: 0.9031 (p) REVERT: D 713 GLU cc_start: 0.8193 (tt0) cc_final: 0.7982 (tm-30) REVERT: D 714 GLN cc_start: 0.8387 (mm110) cc_final: 0.7663 (mm-40) REVERT: D 752 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8372 (tptt) REVERT: D 1131 HIS cc_start: 0.6654 (m-70) cc_final: 0.5823 (m-70) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.1293 time to fit residues: 91.7282 Evaluate side-chains 338 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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: 0.9980 chunk 99 optimal weight: 0.0470 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 118 optimal weight: 0.0470 chunk 140 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN B 714 GLN C 619 ASN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1148 ASN D 435 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.083028 restraints weight = 64138.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.085271 restraints weight = 39417.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.086897 restraints weight = 27609.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088058 restraints weight = 21271.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.088588 restraints weight = 17554.252| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19371 Z= 0.109 Angle : 0.572 15.322 26178 Z= 0.296 Chirality : 0.040 0.155 2925 Planarity : 0.004 0.057 3209 Dihedral : 5.706 85.256 2620 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.82 % 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: -0.61 (0.17), residues: 2380 helix: 0.70 (0.14), residues: 1298 sheet: -1.23 (0.39), residues: 172 loop : -1.85 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 453 TYR 0.025 0.001 TYR A 711 PHE 0.025 0.001 PHE B 623 TRP 0.022 0.001 TRP A1177 HIS 0.006 0.001 HIS B1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (19359) covalent geometry : angle 0.57113 / 0.30 (26154) SS BOND : bond 0.00268 / 0.15 ( 12) SS BOND : angle 1.12878 / 0.70 ( 24) hydrogen bonds : bond 0.03702 / 2.44 ( 918) hydrogen bonds : angle 4.02844 / 2.81 ( 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 465 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 464 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 VAL cc_start: 0.9402 (p) cc_final: 0.9171 (p) REVERT: A 670 MET cc_start: 0.8144 (mmm) cc_final: 0.7876 (mmt) REVERT: A 728 ASP cc_start: 0.8208 (p0) cc_final: 0.7898 (t70) REVERT: A 764 ASN cc_start: 0.8565 (m-40) cc_final: 0.8252 (m110) REVERT: A 1025 ILE cc_start: 0.8845 (mm) cc_final: 0.8546 (mt) REVERT: A 1063 TRP cc_start: 0.7489 (m-90) cc_final: 0.7206 (m-10) REVERT: A 1179 PHE cc_start: 0.8498 (t80) cc_final: 0.7847 (t80) REVERT: A 1190 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8151 (mm-30) REVERT: A 1191 MET cc_start: 0.7653 (tpt) cc_final: 0.7217 (mmt) REVERT: B 444 ILE cc_start: 0.8011 (mm) cc_final: 0.7437 (mt) REVERT: B 474 ILE cc_start: 0.9130 (tt) cc_final: 0.8741 (mm) REVERT: B 481 ILE cc_start: 0.7218 (mm) cc_final: 0.6824 (mm) REVERT: B 527 MET cc_start: 0.7201 (ttt) cc_final: 0.6951 (tpp) REVERT: B 540 LEU cc_start: 0.9185 (tt) cc_final: 0.8928 (tt) REVERT: B 656 LYS cc_start: 0.7456 (tttt) cc_final: 0.7075 (mtpt) REVERT: B 682 PHE cc_start: 0.5162 (m-10) cc_final: 0.4947 (m-10) REVERT: B 697 LYS cc_start: 0.6308 (mmtp) cc_final: 0.5630 (ptmm) REVERT: B 732 TYR cc_start: 0.7652 (m-10) cc_final: 0.7392 (m-10) REVERT: B 766 TRP cc_start: 0.5542 (t-100) cc_final: 0.5262 (t-100) REVERT: B 768 TYR cc_start: 0.7903 (m-10) cc_final: 0.7468 (m-80) REVERT: B 1114 LEU cc_start: 0.8531 (mp) cc_final: 0.8252 (mp) REVERT: B 1186 PHE cc_start: 0.7662 (t80) cc_final: 0.7330 (t80) REVERT: C 406 VAL cc_start: 0.9335 (t) cc_final: 0.8804 (m) REVERT: C 424 TYR cc_start: 0.6883 (t80) cc_final: 0.6465 (t80) REVERT: C 585 MET cc_start: 0.8584 (mmt) cc_final: 0.8104 (mmt) REVERT: C 606 TRP cc_start: 0.8395 (m-10) cc_final: 0.8102 (m-10) REVERT: C 629 MET cc_start: 0.7971 (mtp) cc_final: 0.7605 (tmm) REVERT: C 668 ASP cc_start: 0.8982 (t70) cc_final: 0.8746 (t0) REVERT: C 764 ASN cc_start: 0.8318 (m110) cc_final: 0.7780 (t0) REVERT: C 1030 ASP cc_start: 0.6436 (p0) cc_final: 0.6070 (m-30) REVERT: C 1062 LEU cc_start: 0.7536 (tp) cc_final: 0.6852 (pt) REVERT: C 1064 ARG cc_start: 0.6679 (mpp80) cc_final: 0.6464 (ttt180) REVERT: C 1141 PHE cc_start: 0.8795 (m-80) cc_final: 0.8450 (m-80) REVERT: C 1153 ILE cc_start: 0.9155 (mt) cc_final: 0.8858 (mm) REVERT: C 1175 TYR cc_start: 0.6672 (m-80) cc_final: 0.6445 (m-80) REVERT: C 1195 LEU cc_start: 0.8498 (tt) cc_final: 0.8224 (mm) REVERT: D 463 MET cc_start: 0.7182 (ttm) cc_final: 0.6904 (ttm) REVERT: D 479 LEU cc_start: 0.8584 (mt) cc_final: 0.8227 (mt) REVERT: D 549 TYR cc_start: 0.5866 (p90) cc_final: 0.5069 (t80) REVERT: D 580 SER cc_start: 0.8651 (m) cc_final: 0.8191 (m) REVERT: D 581 LEU cc_start: 0.8782 (tt) cc_final: 0.8500 (tt) REVERT: D 629 MET cc_start: 0.4713 (tpt) cc_final: 0.4442 (mmm) REVERT: D 714 GLN cc_start: 0.8306 (mm110) cc_final: 0.7566 (mm-40) REVERT: D 752 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8366 (tptt) REVERT: D 772 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7369 (mp0) REVERT: D 1042 LYS cc_start: 0.6708 (pttp) cc_final: 0.6475 (mmtt) REVERT: D 1131 HIS cc_start: 0.6613 (m-70) cc_final: 0.6215 (m90) outliers start: 1 outliers final: 0 residues processed: 465 average time/residue: 0.1251 time to fit residues: 94.1482 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 : 0.725 ------------------------------------------------------------------------------- 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: 0.8980 chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 159 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 204 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN B 714 GLN C 435 HIS C 586 GLN C 619 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 714 GLN D1204 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083026 restraints weight = 62935.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.085226 restraints weight = 38517.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.086891 restraints weight = 27107.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.087905 restraints weight = 20760.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.088590 restraints weight = 17243.324| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19371 Z= 0.117 Angle : 0.571 13.103 26178 Z= 0.296 Chirality : 0.041 0.302 2925 Planarity : 0.004 0.056 3209 Dihedral : 5.559 85.099 2620 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 0.92 (0.14), residues: 1305 sheet: -1.02 (0.41), residues: 166 loop : -1.85 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 453 TYR 0.018 0.001 TYR B 421 PHE 0.028 0.001 PHE B1181 TRP 0.051 0.002 TRP A1177 HIS 0.005 0.001 HIS B1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (19359) covalent geometry : angle 0.57042 / 0.30 (26154) SS BOND : bond 0.00210 / 0.12 ( 12) SS BOND : angle 1.29140 / 0.79 ( 24) hydrogen bonds : bond 0.03605 / 2.38 ( 918) hydrogen bonds : angle 4.01570 / 2.81 ( 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 439 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 VAL cc_start: 0.9414 (p) cc_final: 0.9199 (p) REVERT: A 728 ASP cc_start: 0.8235 (p0) cc_final: 0.7930 (t70) REVERT: A 764 ASN cc_start: 0.8563 (m-40) cc_final: 0.8257 (m110) REVERT: A 1025 ILE cc_start: 0.8875 (mm) cc_final: 0.8595 (mt) REVERT: A 1063 TRP cc_start: 0.7579 (m-90) cc_final: 0.7249 (m-10) REVERT: A 1177 TRP cc_start: 0.6220 (p-90) cc_final: 0.5535 (p-90) REVERT: A 1190 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8207 (mm-30) REVERT: A 1191 MET cc_start: 0.7736 (tpt) cc_final: 0.7201 (mmt) REVERT: A 1195 LEU cc_start: 0.8478 (mt) cc_final: 0.7949 (mt) REVERT: A 1199 MET cc_start: 0.8859 (mtt) cc_final: 0.8592 (mtt) REVERT: B 474 ILE cc_start: 0.9148 (tt) cc_final: 0.8749 (mm) REVERT: B 517 PHE cc_start: 0.8725 (p90) cc_final: 0.8489 (p90) REVERT: B 527 MET cc_start: 0.7187 (ttt) cc_final: 0.6949 (tpp) REVERT: B 540 LEU cc_start: 0.9223 (tt) cc_final: 0.8970 (tt) REVERT: B 697 LYS cc_start: 0.6367 (mmtp) cc_final: 0.5934 (ptmm) REVERT: B 766 TRP cc_start: 0.5584 (t-100) cc_final: 0.5336 (t-100) REVERT: B 768 TYR cc_start: 0.7953 (m-10) cc_final: 0.7504 (m-80) REVERT: C 406 VAL cc_start: 0.9322 (t) cc_final: 0.9088 (t) REVERT: C 424 TYR cc_start: 0.6842 (t80) cc_final: 0.6302 (t80) REVERT: C 425 CYS cc_start: 0.8693 (m) cc_final: 0.8482 (m) REVERT: C 503 MET cc_start: 0.8439 (ppp) cc_final: 0.7936 (ppp) REVERT: C 606 TRP cc_start: 0.8502 (m-10) cc_final: 0.8035 (m-10) REVERT: C 629 MET cc_start: 0.7959 (mtp) cc_final: 0.7617 (tmm) REVERT: C 1030 ASP cc_start: 0.6506 (p0) cc_final: 0.6168 (m-30) REVERT: C 1062 LEU cc_start: 0.7530 (tp) cc_final: 0.6866 (pt) REVERT: C 1064 ARG cc_start: 0.6720 (mpp80) cc_final: 0.6468 (ttt180) REVERT: C 1153 ILE cc_start: 0.9154 (mt) cc_final: 0.8879 (mm) REVERT: C 1195 LEU cc_start: 0.8562 (tt) cc_final: 0.8324 (mm) REVERT: D 549 TYR cc_start: 0.5880 (p90) cc_final: 0.5222 (t80) REVERT: D 580 SER cc_start: 0.8645 (m) cc_final: 0.8245 (p) REVERT: D 597 SER cc_start: 0.9309 (p) cc_final: 0.8940 (p) REVERT: D 772 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7253 (mp0) REVERT: D 1131 HIS cc_start: 0.6502 (m-70) cc_final: 0.5754 (m-70) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1243 time to fit residues: 88.3214 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 : 0.619 ------------------------------------------------------------------------------- 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: 6.9990 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN C 619 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D1206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.098727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081867 restraints weight = 64120.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.084100 restraints weight = 39330.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.085685 restraints weight = 27455.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086649 restraints weight = 21107.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.087465 restraints weight = 17611.263| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19371 Z= 0.142 Angle : 0.581 7.191 26178 Z= 0.304 Chirality : 0.041 0.160 2925 Planarity : 0.004 0.056 3209 Dihedral : 5.620 85.143 2620 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: -0.25 (0.17), residues: 2380 helix: 1.05 (0.14), residues: 1308 sheet: -1.05 (0.41), residues: 162 loop : -1.83 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.021 0.001 TYR C1031 PHE 0.022 0.002 PHE B1186 TRP 0.034 0.001 TRP A1177 HIS 0.006 0.001 HIS D1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (19359) covalent geometry : angle 0.58079 / 0.30 (26154) SS BOND : bond 0.00188 / 0.12 ( 12) SS BOND : angle 0.83681 / 0.53 ( 24) hydrogen bonds : bond 0.03596 / 2.36 ( 918) hydrogen bonds : angle 4.06973 / 2.84 ( 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 433 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.765 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: 0.9422 (p) cc_final: 0.9212 (p) REVERT: A 585 MET cc_start: 0.7661 (mmm) cc_final: 0.7409 (mmm) REVERT: A 619 ASN cc_start: 0.7173 (t160) cc_final: 0.6919 (t0) REVERT: A 730 LYS cc_start: 0.8356 (mttm) cc_final: 0.8124 (mmmm) REVERT: A 764 ASN cc_start: 0.8566 (m-40) cc_final: 0.8276 (m110) REVERT: A 1025 ILE cc_start: 0.8900 (mm) cc_final: 0.8592 (mt) REVERT: A 1063 TRP cc_start: 0.7566 (m-90) cc_final: 0.7068 (m-10) REVERT: A 1064 ARG cc_start: 0.7156 (mpp-170) cc_final: 0.6534 (mtp180) REVERT: A 1177 TRP cc_start: 0.5875 (p-90) cc_final: 0.5616 (p-90) REVERT: A 1190 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8245 (mm-30) REVERT: A 1191 MET cc_start: 0.7706 (tpt) cc_final: 0.7204 (mmt) REVERT: A 1195 LEU cc_start: 0.8504 (mt) cc_final: 0.8213 (mt) REVERT: B 474 ILE cc_start: 0.9109 (tt) cc_final: 0.8717 (mm) REVERT: B 502 ILE cc_start: 0.7354 (mp) cc_final: 0.7125 (mp) REVERT: B 527 MET cc_start: 0.7247 (ttt) cc_final: 0.6996 (tpp) REVERT: B 697 LYS cc_start: 0.6396 (mmtp) cc_final: 0.5757 (ptmm) REVERT: B 755 GLU cc_start: 0.6779 (pp20) cc_final: 0.5920 (tp30) REVERT: B 766 TRP cc_start: 0.5646 (t-100) cc_final: 0.5332 (t-100) REVERT: B 768 TYR cc_start: 0.7920 (m-10) cc_final: 0.7530 (m-80) REVERT: C 424 TYR cc_start: 0.6840 (t80) cc_final: 0.6635 (t80) REVERT: C 503 MET cc_start: 0.8429 (ppp) cc_final: 0.8109 (ppp) REVERT: C 606 TRP cc_start: 0.8492 (m-10) cc_final: 0.8110 (m-10) REVERT: C 629 MET cc_start: 0.7966 (mtp) cc_final: 0.7654 (tmm) REVERT: C 668 ASP cc_start: 0.9063 (t70) cc_final: 0.8837 (t0) REVERT: C 708 MET cc_start: 0.7995 (mmm) cc_final: 0.7780 (mmm) REVERT: C 1030 ASP cc_start: 0.6436 (p0) cc_final: 0.6079 (m-30) REVERT: C 1062 LEU cc_start: 0.7479 (tp) cc_final: 0.6804 (pt) REVERT: C 1064 ARG cc_start: 0.6772 (mpp80) cc_final: 0.6556 (ttt180) REVERT: C 1153 ILE cc_start: 0.9172 (mt) cc_final: 0.8886 (mm) REVERT: C 1191 MET cc_start: 0.7075 (mmm) cc_final: 0.6724 (mmt) REVERT: C 1195 LEU cc_start: 0.8606 (tt) cc_final: 0.8256 (mm) REVERT: D 549 TYR cc_start: 0.5911 (p90) cc_final: 0.5275 (t80) REVERT: D 580 SER cc_start: 0.8578 (m) cc_final: 0.8220 (p) REVERT: D 581 LEU cc_start: 0.8752 (tt) cc_final: 0.8515 (tt) REVERT: D 597 SER cc_start: 0.9307 (p) cc_final: 0.8950 (p) REVERT: D 629 MET cc_start: 0.4877 (tpt) cc_final: 0.4582 (mmm) REVERT: D 670 MET cc_start: 0.8067 (mtt) cc_final: 0.7864 (mtt) REVERT: D 772 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7219 (mp0) REVERT: D 1057 MET cc_start: 0.5162 (ttp) cc_final: 0.4839 (ttp) REVERT: D 1116 MET cc_start: 0.8010 (mmm) cc_final: 0.7568 (mpp) REVERT: D 1131 HIS cc_start: 0.6535 (m-70) cc_final: 0.5829 (m-70) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.1210 time to fit residues: 85.5757 Evaluate side-chains 344 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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: 0.9990 chunk 112 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 105 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 217 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN A 709 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN C 619 ASN C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.099987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082675 restraints weight = 63991.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.084919 restraints weight = 39576.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.086447 restraints weight = 27827.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.087532 restraints weight = 21716.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088304 restraints weight = 18105.729| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19371 Z= 0.118 Angle : 0.585 10.402 26178 Z= 0.302 Chirality : 0.041 0.171 2925 Planarity : 0.004 0.064 3209 Dihedral : 5.492 83.442 2620 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -0.18 (0.17), residues: 2380 helix: 1.12 (0.14), residues: 1308 sheet: -1.01 (0.42), residues: 156 loop : -1.83 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 453 TYR 0.018 0.001 TYR C1031 PHE 0.023 0.002 PHE B1181 TRP 0.027 0.001 TRP A1177 HIS 0.004 0.001 HIS B1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (19359) covalent geometry : angle 0.58337 / 0.30 (26154) SS BOND : bond 0.00235 / 0.16 ( 12) SS BOND : angle 1.71162 / 1.05 ( 24) hydrogen bonds : bond 0.03469 / 2.29 ( 918) hydrogen bonds : angle 3.97444 / 2.78 ( 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 440 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.849 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: 0.8525 (t) cc_final: 0.8308 (t) REVERT: A 730 LYS cc_start: 0.8466 (mttm) cc_final: 0.8128 (mmmm) REVERT: A 764 ASN cc_start: 0.8535 (m-40) cc_final: 0.8062 (m110) REVERT: A 1025 ILE cc_start: 0.8862 (mm) cc_final: 0.8569 (mt) REVERT: A 1063 TRP cc_start: 0.7497 (m-90) cc_final: 0.7097 (m-10) REVERT: A 1064 ARG cc_start: 0.6832 (mpp-170) cc_final: 0.6449 (mtp180) REVERT: A 1177 TRP cc_start: 0.6106 (p-90) cc_final: 0.5726 (p-90) REVERT: A 1190 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8276 (mm-30) REVERT: A 1191 MET cc_start: 0.7744 (tpt) cc_final: 0.7241 (mmt) REVERT: A 1195 LEU cc_start: 0.8462 (mt) cc_final: 0.8248 (mt) REVERT: B 474 ILE cc_start: 0.9141 (tt) cc_final: 0.8728 (mm) REVERT: B 527 MET cc_start: 0.7256 (ttt) cc_final: 0.6986 (tpp) REVERT: B 571 PHE cc_start: 0.7721 (m-80) cc_final: 0.7435 (m-80) REVERT: B 585 MET cc_start: 0.8739 (mmm) cc_final: 0.8448 (mmp) REVERT: B 667 PHE cc_start: 0.8075 (m-80) cc_final: 0.7834 (m-10) REVERT: B 697 LYS cc_start: 0.6476 (mmtp) cc_final: 0.5800 (ptmm) REVERT: B 707 THR cc_start: 0.8965 (p) cc_final: 0.8628 (t) REVERT: B 755 GLU cc_start: 0.6813 (pp20) cc_final: 0.5961 (tp30) REVERT: B 766 TRP cc_start: 0.5494 (t-100) cc_final: 0.5260 (t-100) REVERT: B 768 TYR cc_start: 0.8018 (m-10) cc_final: 0.7594 (m-80) REVERT: C 424 TYR cc_start: 0.6791 (t80) cc_final: 0.6429 (t80) REVERT: C 503 MET cc_start: 0.8453 (ppp) cc_final: 0.8121 (ppp) REVERT: C 585 MET cc_start: 0.8972 (mmt) cc_final: 0.8406 (mmt) REVERT: C 606 TRP cc_start: 0.8465 (m-10) cc_final: 0.8106 (m-10) REVERT: C 629 MET cc_start: 0.7955 (mtp) cc_final: 0.7644 (tmm) REVERT: C 668 ASP cc_start: 0.9052 (t70) cc_final: 0.8841 (t0) REVERT: C 708 MET cc_start: 0.7966 (mmm) cc_final: 0.7732 (mmm) REVERT: C 1030 ASP cc_start: 0.6407 (p0) cc_final: 0.6125 (m-30) REVERT: C 1062 LEU cc_start: 0.7509 (tp) cc_final: 0.6834 (pt) REVERT: C 1064 ARG cc_start: 0.6801 (mpp80) cc_final: 0.6466 (ttt180) REVERT: C 1153 ILE cc_start: 0.9177 (mt) cc_final: 0.8960 (mt) REVERT: C 1195 LEU cc_start: 0.8595 (tt) cc_final: 0.8313 (mm) REVERT: D 405 TYR cc_start: 0.7343 (m-80) cc_final: 0.7124 (m-80) REVERT: D 549 TYR cc_start: 0.5926 (p90) cc_final: 0.5343 (t80) REVERT: D 580 SER cc_start: 0.8581 (m) cc_final: 0.8172 (p) REVERT: D 581 LEU cc_start: 0.8727 (tt) cc_final: 0.8368 (tt) REVERT: D 629 MET cc_start: 0.4767 (tpt) cc_final: 0.4509 (mmm) REVERT: D 674 MET cc_start: 0.7921 (mmm) cc_final: 0.7674 (tpp) REVERT: D 1057 MET cc_start: 0.5179 (ttp) cc_final: 0.4844 (ttp) REVERT: D 1131 HIS cc_start: 0.6571 (m-70) cc_final: 0.6011 (m-70) REVERT: D 1197 VAL cc_start: 0.8812 (t) cc_final: 0.8589 (t) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.1256 time to fit residues: 90.1961 Evaluate side-chains 345 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 179 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 165 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 chunk 210 optimal weight: 0.1980 chunk 174 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 756 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B1131 HIS C 619 ASN C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.083843 restraints weight = 63285.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.086122 restraints weight = 38893.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.087733 restraints weight = 27417.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.088692 restraints weight = 21291.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.089477 restraints weight = 17924.270| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19371 Z= 0.106 Angle : 0.568 8.379 26178 Z= 0.289 Chirality : 0.040 0.162 2925 Planarity : 0.004 0.056 3209 Dihedral : 5.296 82.303 2620 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.01 (0.17), residues: 2380 helix: 1.28 (0.15), residues: 1302 sheet: -0.95 (0.42), residues: 157 loop : -1.76 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 453 TYR 0.014 0.001 TYR C1031 PHE 0.022 0.001 PHE B1186 TRP 0.023 0.001 TRP A1177 HIS 0.004 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (19359) covalent geometry : angle 0.56806 / 0.29 (26154) SS BOND : bond 0.00300 / 0.17 ( 12) SS BOND : angle 0.87075 / 0.55 ( 24) hydrogen bonds : bond 0.03317 / 2.18 ( 918) hydrogen bonds : angle 3.89902 / 2.72 ( 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 449 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8468 (t) cc_final: 0.8265 (t) REVERT: A 527 MET cc_start: 0.8009 (ttm) cc_final: 0.7708 (ttp) REVERT: A 538 VAL cc_start: 0.9395 (p) cc_final: 0.9133 (p) REVERT: A 586 GLN cc_start: 0.7841 (mt0) cc_final: 0.7584 (mt0) REVERT: A 708 MET cc_start: 0.8183 (mmt) cc_final: 0.7820 (mmt) REVERT: A 730 LYS cc_start: 0.8488 (mttm) cc_final: 0.8191 (mtpp) REVERT: A 764 ASN cc_start: 0.8582 (m-40) cc_final: 0.8216 (m110) REVERT: A 1025 ILE cc_start: 0.8866 (mm) cc_final: 0.8564 (mt) REVERT: A 1063 TRP cc_start: 0.7549 (m-90) cc_final: 0.7164 (m-10) REVERT: A 1064 ARG cc_start: 0.6874 (mpp-170) cc_final: 0.6469 (mtp180) REVERT: A 1190 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8276 (mm-30) REVERT: A 1191 MET cc_start: 0.7735 (tpt) cc_final: 0.7254 (mmt) REVERT: B 474 ILE cc_start: 0.9113 (tt) cc_final: 0.8737 (mm) REVERT: B 517 PHE cc_start: 0.8605 (p90) cc_final: 0.8269 (p90) REVERT: B 527 MET cc_start: 0.7178 (ttt) cc_final: 0.6940 (tpp) REVERT: B 540 LEU cc_start: 0.9185 (tt) cc_final: 0.8938 (tt) REVERT: B 585 MET cc_start: 0.8726 (mmm) cc_final: 0.8376 (mmp) REVERT: B 587 GLN cc_start: 0.7842 (mm110) cc_final: 0.7248 (mt0) REVERT: B 667 PHE cc_start: 0.7968 (m-80) cc_final: 0.7763 (m-10) REVERT: B 697 LYS cc_start: 0.6449 (mmtp) cc_final: 0.5896 (ptmm) REVERT: B 707 THR cc_start: 0.8964 (p) cc_final: 0.8619 (t) REVERT: B 755 GLU cc_start: 0.6877 (pp20) cc_final: 0.6043 (tp30) REVERT: B 768 TYR cc_start: 0.7942 (m-10) cc_final: 0.7523 (m-80) REVERT: C 424 TYR cc_start: 0.6730 (t80) cc_final: 0.6305 (t80) REVERT: C 503 MET cc_start: 0.8464 (ppp) cc_final: 0.8120 (ppp) REVERT: C 585 MET cc_start: 0.8971 (mmt) cc_final: 0.8371 (mmt) REVERT: C 606 TRP cc_start: 0.8474 (m-10) cc_final: 0.8164 (m-10) REVERT: C 629 MET cc_start: 0.7927 (mtp) cc_final: 0.7655 (tmm) REVERT: C 708 MET cc_start: 0.7940 (mmm) cc_final: 0.7692 (mmm) REVERT: C 1062 LEU cc_start: 0.7488 (tp) cc_final: 0.6837 (pt) REVERT: C 1064 ARG cc_start: 0.6794 (mpp80) cc_final: 0.6478 (ttt180) REVERT: C 1153 ILE cc_start: 0.9167 (mt) cc_final: 0.8957 (mt) REVERT: C 1195 LEU cc_start: 0.8535 (tt) cc_final: 0.8270 (mm) REVERT: D 549 TYR cc_start: 0.5819 (p90) cc_final: 0.5333 (t80) REVERT: D 580 SER cc_start: 0.8595 (m) cc_final: 0.8200 (p) REVERT: D 629 MET cc_start: 0.4749 (tpt) cc_final: 0.4472 (mmm) REVERT: D 674 MET cc_start: 0.7998 (mmm) cc_final: 0.7741 (mmm) REVERT: D 1057 MET cc_start: 0.5274 (ttp) cc_final: 0.4903 (ttp) REVERT: D 1116 MET cc_start: 0.7875 (mmm) cc_final: 0.7589 (mpp) REVERT: D 1131 HIS cc_start: 0.6454 (m-70) cc_final: 0.5840 (m90) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.1224 time to fit residues: 90.1360 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 : 0.815 ------------------------------------------------------------------------------- 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: 5.9990 chunk 38 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 217 optimal weight: 0.0010 chunk 181 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 195 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 overall best weight: 3.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN A 709 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 HIS ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN C 619 ASN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.096968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.079769 restraints weight = 65388.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.081990 restraints weight = 40385.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.083551 restraints weight = 28409.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.084494 restraints weight = 21966.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.085279 restraints weight = 18413.897| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.5369 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= 0.221 Angle : 0.709 13.680 26178 Z= 0.367 Chirality : 0.044 0.201 2925 Planarity : 0.004 0.053 3209 Dihedral : 5.812 88.442 2620 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 0.99 (0.14), residues: 1304 sheet: -1.24 (0.39), residues: 174 loop : -1.87 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 453 TYR 0.026 0.002 TYR C1031 PHE 0.027 0.002 PHE C1200 TRP 0.069 0.002 TRP A1177 HIS 0.007 0.002 HIS D1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (19359) covalent geometry : angle 0.70849 / 0.37 (26154) SS BOND : bond 0.00324 / 0.20 ( 12) SS BOND : angle 1.25928 / 0.78 ( 24) hydrogen bonds : bond 0.03894 / 2.56 ( 918) hydrogen bonds : angle 4.31811 / 2.98 ( 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 413 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8452 (t) cc_final: 0.8237 (t) REVERT: A 483 LEU cc_start: 0.8632 (tp) cc_final: 0.8366 (tp) REVERT: A 619 ASN cc_start: 0.6962 (t160) cc_final: 0.6729 (t0) REVERT: A 730 LYS cc_start: 0.8450 (mttm) cc_final: 0.8103 (mmmm) REVERT: A 764 ASN cc_start: 0.8640 (m-40) cc_final: 0.8346 (m110) REVERT: A 1025 ILE cc_start: 0.8903 (mm) cc_final: 0.8601 (mt) REVERT: A 1063 TRP cc_start: 0.7401 (m-90) cc_final: 0.7190 (m-10) REVERT: A 1064 ARG cc_start: 0.6833 (mpp-170) cc_final: 0.6502 (mtp180) REVERT: A 1177 TRP cc_start: 0.6282 (p-90) cc_final: 0.5727 (p-90) REVERT: A 1190 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8392 (mm-30) REVERT: A 1191 MET cc_start: 0.7648 (tpt) cc_final: 0.7192 (mmt) REVERT: B 474 ILE cc_start: 0.9143 (tt) cc_final: 0.8718 (mm) REVERT: B 527 MET cc_start: 0.7405 (ttt) cc_final: 0.7106 (tpp) REVERT: B 697 LYS cc_start: 0.6664 (mmtp) cc_final: 0.6140 (ptmm) REVERT: B 707 THR cc_start: 0.9017 (p) cc_final: 0.8674 (t) REVERT: B 755 GLU cc_start: 0.6908 (pp20) cc_final: 0.6146 (tp30) REVERT: B 766 TRP cc_start: 0.6071 (t-100) cc_final: 0.5477 (t-100) REVERT: B 768 TYR cc_start: 0.7992 (m-10) cc_final: 0.7499 (m-80) REVERT: C 424 TYR cc_start: 0.6912 (t80) cc_final: 0.6650 (t80) REVERT: C 503 MET cc_start: 0.8505 (ppp) cc_final: 0.8077 (ppp) REVERT: C 585 MET cc_start: 0.8996 (mmt) cc_final: 0.8474 (mmt) REVERT: C 629 MET cc_start: 0.8072 (mtp) cc_final: 0.7660 (tmm) REVERT: C 668 ASP cc_start: 0.9082 (t70) cc_final: 0.8831 (t0) REVERT: C 708 MET cc_start: 0.7918 (mmm) cc_final: 0.7666 (mmm) REVERT: C 1064 ARG cc_start: 0.7373 (mpp80) cc_final: 0.6582 (ttt180) REVERT: C 1153 ILE cc_start: 0.9206 (mt) cc_final: 0.8931 (mm) REVERT: C 1195 LEU cc_start: 0.8572 (tt) cc_final: 0.8201 (mm) REVERT: D 541 PHE cc_start: 0.8232 (t80) cc_final: 0.8026 (t80) REVERT: D 549 TYR cc_start: 0.6026 (p90) cc_final: 0.5496 (t80) REVERT: D 580 SER cc_start: 0.8549 (m) cc_final: 0.8161 (p) REVERT: D 581 LEU cc_start: 0.8791 (tt) cc_final: 0.8181 (tt) REVERT: D 607 PHE cc_start: 0.8268 (t80) cc_final: 0.7850 (t80) REVERT: D 629 MET cc_start: 0.4940 (tpt) cc_final: 0.4696 (mmm) REVERT: D 674 MET cc_start: 0.8025 (mmm) cc_final: 0.7600 (mmm) REVERT: D 1057 MET cc_start: 0.5051 (ttp) cc_final: 0.4700 (ttp) REVERT: D 1116 MET cc_start: 0.7942 (mmm) cc_final: 0.7533 (mpp) REVERT: D 1131 HIS cc_start: 0.6703 (m-70) cc_final: 0.5923 (m-70) REVERT: D 1197 VAL cc_start: 0.8844 (t) cc_final: 0.8636 (t) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.1238 time to fit residues: 83.4470 Evaluate side-chains 325 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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: 0.0050 chunk 150 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 207 optimal weight: 9.9990 chunk 135 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 209 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN A 709 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C1131 HIS C1148 ASN C1204 HIS D 435 HIS D 642 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.083155 restraints weight = 63278.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.085487 restraints weight = 38455.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087097 restraints weight = 26712.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.088113 restraints weight = 20486.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.088904 restraints weight = 16994.108| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19371 Z= 0.113 Angle : 0.600 8.964 26178 Z= 0.307 Chirality : 0.041 0.187 2925 Planarity : 0.004 0.054 3209 Dihedral : 5.497 84.358 2620 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.17), residues: 2380 helix: 1.30 (0.15), residues: 1300 sheet: -1.06 (0.42), residues: 159 loop : -1.72 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 453 TYR 0.015 0.001 TYR C1031 PHE 0.032 0.001 PHE C1082 TRP 0.046 0.002 TRP A1177 HIS 0.007 0.001 HIS B1204 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (19359) covalent geometry : angle 0.59835 / 0.31 (26154) SS BOND : bond 0.00291 / 0.16 ( 12) SS BOND : angle 1.38211 / 0.79 ( 24) hydrogen bonds : bond 0.03404 / 2.24 ( 918) hydrogen bonds : angle 3.96623 / 2.76 ( 2682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.90 seconds wall clock time: 55 minutes 53.08 seconds (3353.08 seconds total)