Starting phenix.real_space_refine on Thu Mar 5 03:32:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uy6_26865/03_2026/7uy6_26865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uy6_26865/03_2026/7uy6_26865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uy6_26865/03_2026/7uy6_26865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uy6_26865/03_2026/7uy6_26865.map" model { file = "/net/cci-nas-00/data/ceres_data/7uy6_26865/03_2026/7uy6_26865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uy6_26865/03_2026/7uy6_26865.cif" } resolution = 2.9 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= 0.004 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 170 5.49 5 S 65 5.16 5 C 11367 2.51 5 N 3166 2.21 5 O 3977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18746 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1367 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 7, 'GLN:plan1': 3, 'TYR:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 8542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8542 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 22, 'TRANS': 989} Chain breaks: 3 Chain: "D" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "E" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1195 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 952 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1542 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 1, 'TRANS': 182} Chain: "B" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3293 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 24, 'rna3p_pur': 62, 'rna3p_pyr': 57} Link IDs: {'rna2p': 36, 'rna3p': 119} Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10290 SG CYS D 555 76.519 71.540 85.390 1.00102.65 S ATOM 10303 SG CYS D 557 74.797 69.232 87.751 1.00107.36 S ATOM 10423 SG CYS D 572 72.846 70.796 84.821 1.00101.57 S ATOM 10444 SG CYS D 575 73.748 72.898 87.764 1.00108.23 S Time building chain proxies: 4.33, per 1000 atoms: 0.23 Number of scatterers: 18746 At special positions: 0 Unit cell: (151.8, 158.4, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 65 16.00 P 170 15.00 O 3977 8.00 N 3166 7.00 C 11367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.50 Conformation dependent library (CDL) restraints added in 695.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 900 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 572 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 557 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 555 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 575 " Number of angles added : 6 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 16 sheets defined 49.4% alpha, 21.4% beta 28 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'H' and resid 115 through 130 Processing helix chain 'H' and resid 131 through 139 removed outlier: 3.836A pdb=" N HIS H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 148 Processing helix chain 'H' and resid 157 through 161 removed outlier: 3.560A pdb=" N LYS H 160 " --> pdb=" O VAL H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 Processing helix chain 'H' and resid 203 through 216 removed outlier: 4.323A pdb=" N GLU H 216 " --> pdb=" O ASP H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 400 removed outlier: 3.620A pdb=" N VAL H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 403 No H-bonds generated for 'chain 'H' and resid 401 through 403' Processing helix chain 'H' and resid 469 through 480 removed outlier: 4.093A pdb=" N ARG H 473 " --> pdb=" O SER H 469 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN H 477 " --> pdb=" O ARG H 473 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS H 478 " --> pdb=" O LEU H 474 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 480 " --> pdb=" O ILE H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 531 Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.533A pdb=" N GLY A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.503A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 144 through 155 removed outlier: 4.292A pdb=" N TYR A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.634A pdb=" N PHE A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.877A pdb=" N SER A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.508A pdb=" N ARG A 304 " --> pdb=" O CYS A 300 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.616A pdb=" N ASN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.809A pdb=" N LYS A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 425 through 426 No H-bonds generated for 'chain 'A' and resid 425 through 426' Processing helix chain 'A' and resid 427 through 431 Processing helix chain 'A' and resid 444 through 467 removed outlier: 3.540A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.920A pdb=" N GLU A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.964A pdb=" N ASN A 556 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 557 " --> pdb=" O GLN A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 557' Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 565 through 579 removed outlier: 3.701A pdb=" N ASP A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.880A pdb=" N ILE A 626 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.735A pdb=" N LYS A 717 " --> pdb=" O GLN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 793 removed outlier: 3.608A pdb=" N LEU A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 804 removed outlier: 4.092A pdb=" N LYS A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.520A pdb=" N GLN A 901 " --> pdb=" O GLN A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 911 through 926 Processing helix chain 'A' and resid 938 through 965 removed outlier: 3.687A pdb=" N MET A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) Proline residue: A 959 - end of helix Processing helix chain 'A' and resid 966 through 967 No H-bonds generated for 'chain 'A' and resid 966 through 967' Processing helix chain 'A' and resid 968 through 971 removed outlier: 3.641A pdb=" N LYS A 971 " --> pdb=" O ASP A 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 968 through 971' Processing helix chain 'A' and resid 972 through 980 removed outlier: 4.543A pdb=" N GLN A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1009 Processing helix chain 'A' and resid 1014 through 1038 Processing helix chain 'A' and resid 1045 through 1075 removed outlier: 3.959A pdb=" N LYS A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A1050 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1094 Processing helix chain 'A' and resid 1103 through 1108 Processing helix chain 'D' and resid 516 through 527 Processing helix chain 'D' and resid 603 through 615 Processing helix chain 'D' and resid 621 through 634 removed outlier: 4.583A pdb=" N GLN D 625 " --> pdb=" O GLN D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 679 through 697 removed outlier: 4.320A pdb=" N GLU D 683 " --> pdb=" O ASN D 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 110 through 123 removed outlier: 3.540A pdb=" N TYR E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 175 removed outlier: 4.140A pdb=" N SER E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 22 removed outlier: 3.519A pdb=" N MET F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 Processing helix chain 'F' and resid 114 through 119 removed outlier: 3.836A pdb=" N PHE F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.774A pdb=" N LYS G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 removed outlier: 3.623A pdb=" N ILE G 41 " --> pdb=" O LYS G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 removed outlier: 4.037A pdb=" N LEU G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA G 94 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 157 removed outlier: 3.606A pdb=" N LYS G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 184 Processing sheet with id=AA1, first strand: chain 'H' and resid 220 through 221 removed outlier: 3.779A pdb=" N LYS H 230 " --> pdb=" O LYS H 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 406 through 411 removed outlier: 4.085A pdb=" N LYS H 382 " --> pdb=" O ILE H 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.747A pdb=" N VAL A 157 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ALA A 170 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.747A pdb=" N VAL A 157 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ALA A 170 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 115 Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.776A pdb=" N GLY A 531 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 808 through 813 removed outlier: 3.554A pdb=" N LEU A 617 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP A 618 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS A 849 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 850 " --> pdb=" O SER A 869 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 874 through 876 Processing sheet with id=AB1, first strand: chain 'D' and resid 532 through 545 removed outlier: 5.617A pdb=" N LEU D 541 " --> pdb=" O GLN D 592 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN D 592 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SER D 543 " --> pdb=" O PHE D 590 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE D 590 " --> pdb=" O SER D 543 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG D 588 " --> pdb=" O GLN D 545 " (cutoff:3.500A) removed outlier: 13.501A pdb=" N THR D 597 " --> pdb=" O ILE D 668 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N TYR D 670 " --> pdb=" O THR D 597 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL D 672 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET D 601 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LYS D 674 " --> pdb=" O MET D 601 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU D 654 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE D 675 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE D 652 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 649 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 533 " --> pdb=" O PHE D 657 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 551 through 554 removed outlier: 3.588A pdb=" N GLN D 582 " --> pdb=" O ARG D 554 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 562 through 564 removed outlier: 3.897A pdb=" N PHE D 571 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 66 through 76 removed outlier: 4.257A pdb=" N MET E 86 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 98 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE E 142 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN E 101 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N TYR E 146 " --> pdb=" O GLN E 101 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU E 144 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS E 135 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR E 146 " --> pdb=" O MET E 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 87 through 91 removed outlier: 3.809A pdb=" N GLU F 72 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N VAL F 83 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 55 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU F 41 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F 26 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 71 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 46 through 51 removed outlier: 7.144A pdb=" N LEU G 46 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR G 116 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER G 103 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE G 58 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN G 73 " --> pdb=" O GLN G 63 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS G 65 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 71 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS G 80 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 46 through 51 removed outlier: 7.144A pdb=" N LEU G 46 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR G 116 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER G 103 " --> pdb=" O ASP G 134 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP G 134 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL G 105 " --> pdb=" O CYS G 132 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS G 132 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE G 107 " --> pdb=" O MET G 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET G 130 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN G 109 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 21.376A pdb=" N LYS G 80 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 16.095A pdb=" N ILE G 123 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N ILE G 82 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU G 125 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS G 80 " --> pdb=" O LEU G 146 " (cutoff:3.500A) 754 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4358 1.33 - 1.45: 4756 1.45 - 1.57: 9896 1.57 - 1.69: 338 1.69 - 1.81: 97 Bond restraints: 19445 Sorted by residual: bond pdb=" C THR A 814 " pdb=" O THR A 814 " ideal model delta sigma weight residual 1.243 1.226 0.017 9.50e-03 1.11e+04 3.38e+00 bond pdb=" CG1 ILE A 376 " pdb=" CD1 ILE A 376 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.77e+00 bond pdb=" CA THR A 814 " pdb=" CB THR A 814 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.53e-02 4.27e+03 1.28e+00 bond pdb=" CA ILE A1104 " pdb=" CB ILE A1104 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.05e+00 bond pdb=" CB PRO E 28 " pdb=" CG PRO E 28 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.18e-01 ... (remaining 19440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 26472 1.27 - 2.53: 434 2.53 - 3.80: 60 3.80 - 5.06: 23 5.06 - 6.33: 13 Bond angle restraints: 27002 Sorted by residual: angle pdb=" CA THR A 814 " pdb=" C THR A 814 " pdb=" N ASP A 815 " ideal model delta sigma weight residual 119.98 116.56 3.42 8.50e-01 1.38e+00 1.62e+01 angle pdb=" N ASP A 816 " pdb=" CA ASP A 816 " pdb=" C ASP A 816 " ideal model delta sigma weight residual 109.24 114.57 -5.33 1.63e+00 3.76e-01 1.07e+01 angle pdb=" N LEU A 813 " pdb=" CA LEU A 813 " pdb=" C LEU A 813 " ideal model delta sigma weight residual 108.52 103.45 5.07 1.63e+00 3.76e-01 9.66e+00 angle pdb=" C THR A 814 " pdb=" CA THR A 814 " pdb=" CB THR A 814 " ideal model delta sigma weight residual 117.23 113.42 3.81 1.36e+00 5.41e-01 7.83e+00 angle pdb=" C TRP A 876 " pdb=" N ILE A 877 " pdb=" CA ILE A 877 " ideal model delta sigma weight residual 121.97 126.43 -4.46 1.80e+00 3.09e-01 6.14e+00 ... (remaining 26997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 11318 35.72 - 71.44: 487 71.44 - 107.16: 61 107.16 - 142.88: 0 142.88 - 178.60: 8 Dihedral angle restraints: 11874 sinusoidal: 6366 harmonic: 5508 Sorted by residual: dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 200.00 21.40 178.60 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C B 43 " pdb=" C1' C B 43 " pdb=" N1 C B 43 " pdb=" C2 C B 43 " ideal model delta sinusoidal sigma weight residual 200.00 39.35 160.65 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' U B 158 " pdb=" C1' U B 158 " pdb=" N1 U B 158 " pdb=" C2 U B 158 " ideal model delta sinusoidal sigma weight residual -128.00 50.10 -178.10 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 11871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2484 0.041 - 0.082: 475 0.082 - 0.123: 142 0.123 - 0.164: 9 0.164 - 0.205: 3 Chirality restraints: 3113 Sorted by residual: chirality pdb=" CG LEU A 920 " pdb=" CB LEU A 920 " pdb=" CD1 LEU A 920 " pdb=" CD2 LEU A 920 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LEU A 813 " pdb=" N LEU A 813 " pdb=" C LEU A 813 " pdb=" CB LEU A 813 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA THR A 814 " pdb=" N THR A 814 " pdb=" C THR A 814 " pdb=" CB THR A 814 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3110 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1104 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A1105 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A1105 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1105 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 588 " -0.092 9.50e-02 1.11e+02 4.14e-02 1.18e+00 pdb=" NE ARG D 588 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG D 588 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG D 588 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 588 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 924 " -0.008 2.00e-02 2.50e+03 7.74e-03 1.05e+00 pdb=" CG PHE A 924 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE A 924 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 924 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 924 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 924 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 924 " -0.002 2.00e-02 2.50e+03 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2114 2.75 - 3.29: 17264 3.29 - 3.83: 30683 3.83 - 4.36: 36344 4.36 - 4.90: 60190 Nonbonded interactions: 146595 Sorted by model distance: nonbonded pdb=" OH TYR A1061 " pdb=" O2' G B 61 " model vdw 2.215 3.040 nonbonded pdb=" O GLN A 228 " pdb=" NH1 ARG A 473 " model vdw 2.245 3.120 nonbonded pdb=" O2' U B 41 " pdb=" OP1 C B 43 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLN A1008 " pdb=" OH TYR A1025 " model vdw 2.272 3.040 nonbonded pdb=" OE1 GLN A 417 " pdb=" OH TYR A 422 " model vdw 2.283 3.040 ... (remaining 146590 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.390 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.780 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.002 0.052 19449 Z= 0.103 Angle : 0.444 6.325 27008 Z= 0.243 Chirality : 0.036 0.205 3113 Planarity : 0.003 0.041 2835 Dihedral : 18.325 178.601 8294 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.06 % Allowed : 0.30 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.20), residues: 1823 helix: 2.06 (0.19), residues: 790 sheet: 0.07 (0.31), residues: 287 loop : -0.24 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 588 TYR 0.015 0.001 TYR A 490 PHE 0.018 0.001 PHE A 924 TRP 0.013 0.001 TRP A 496 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00215 (19445) covalent geometry : angle 0.44253 (27002) hydrogen bonds : bond 0.19097 ( 799) hydrogen bonds : angle 6.67151 ( 2292) metal coordination : bond 0.00299 ( 4) metal coordination : angle 2.61945 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: H 472 GLN cc_start: 0.3963 (tp40) cc_final: 0.3237 (tm130) REVERT: A 689 ASN cc_start: 0.7768 (m-40) cc_final: 0.7475 (p0) outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 0.6932 time to fit residues: 203.2648 Evaluate side-chains 191 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 484 ASN H 512 ASN A 55 GLN A 102 ASN A 294 GLN A 734 GLN A 865 HIS D 693 HIS E 169 GLN F 7 GLN F 31 ASN F 110 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.168992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114252 restraints weight = 23969.917| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.11 r_work: 0.3082 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19449 Z= 0.123 Angle : 0.513 6.488 27008 Z= 0.276 Chirality : 0.038 0.153 3113 Planarity : 0.003 0.029 2835 Dihedral : 19.240 179.161 4451 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.87 % Allowed : 8.49 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.20), residues: 1823 helix: 2.16 (0.19), residues: 802 sheet: 0.25 (0.32), residues: 278 loop : -0.29 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 49 TYR 0.018 0.001 TYR A 490 PHE 0.016 0.001 PHE H 524 TRP 0.014 0.002 TRP A 496 HIS 0.009 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00268 (19445) covalent geometry : angle 0.51035 (27002) hydrogen bonds : bond 0.05174 ( 799) hydrogen bonds : angle 4.45611 ( 2292) metal coordination : bond 0.00555 ( 4) metal coordination : angle 3.21975 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.636 Fit side-chains REVERT: H 385 ASN cc_start: 0.4913 (OUTLIER) cc_final: 0.4663 (p0) REVERT: H 472 GLN cc_start: 0.4124 (tp40) cc_final: 0.3506 (tm130) REVERT: H 490 GLU cc_start: 0.5444 (tp30) cc_final: 0.5212 (tp30) REVERT: H 521 PHE cc_start: 0.5048 (OUTLIER) cc_final: 0.4339 (m-10) REVERT: A 566 MET cc_start: 0.8188 (tpp) cc_final: 0.7827 (mmp) REVERT: A 589 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7899 (p0) REVERT: A 643 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7757 (t0) REVERT: A 897 GLN cc_start: 0.8314 (mp-120) cc_final: 0.8086 (tm-30) REVERT: D 549 LYS cc_start: 0.8274 (tptp) cc_final: 0.8026 (tptp) REVERT: D 588 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7330 (mtm-85) REVERT: E 86 MET cc_start: 0.8099 (mmt) cc_final: 0.7835 (mmm) REVERT: E 119 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7394 (tm-30) REVERT: E 148 SER cc_start: 0.8595 (p) cc_final: 0.8330 (m) REVERT: E 169 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7728 (mt0) outliers start: 31 outliers final: 13 residues processed: 216 average time/residue: 0.6568 time to fit residues: 158.3911 Evaluate side-chains 211 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 461 GLN H 467 GLN H 484 ASN A 55 GLN A 865 HIS D 619 HIS D 693 HIS E 40 ASN F 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.167810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113292 restraints weight = 24085.301| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.10 r_work: 0.3062 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 19449 Z= 0.134 Angle : 0.507 7.063 27008 Z= 0.273 Chirality : 0.038 0.153 3113 Planarity : 0.003 0.026 2835 Dihedral : 19.237 178.449 4451 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.47 % Allowed : 10.72 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.20), residues: 1823 helix: 2.12 (0.19), residues: 805 sheet: 0.25 (0.31), residues: 274 loop : -0.31 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 49 TYR 0.018 0.001 TYR A 490 PHE 0.018 0.001 PHE H 526 TRP 0.015 0.002 TRP A 496 HIS 0.012 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00306 (19445) covalent geometry : angle 0.50429 (27002) hydrogen bonds : bond 0.05106 ( 799) hydrogen bonds : angle 4.21709 ( 2292) metal coordination : bond 0.00709 ( 4) metal coordination : angle 3.53257 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 385 ASN cc_start: 0.4652 (OUTLIER) cc_final: 0.4349 (p0) REVERT: H 396 VAL cc_start: 0.6644 (OUTLIER) cc_final: 0.6410 (p) REVERT: H 402 LEU cc_start: 0.6606 (mm) cc_final: 0.6022 (mt) REVERT: H 472 GLN cc_start: 0.4224 (tp40) cc_final: 0.3592 (tm130) REVERT: H 479 LEU cc_start: 0.5113 (tt) cc_final: 0.4714 (mt) REVERT: H 490 GLU cc_start: 0.5616 (tp30) cc_final: 0.5296 (tp30) REVERT: H 521 PHE cc_start: 0.5205 (OUTLIER) cc_final: 0.4573 (m-10) REVERT: A 566 MET cc_start: 0.8260 (tpp) cc_final: 0.7938 (mmp) REVERT: A 602 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: A 643 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7869 (t70) REVERT: A 848 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7561 (mp-120) REVERT: D 588 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7844 (mtm-85) REVERT: E 86 MET cc_start: 0.8122 (mmt) cc_final: 0.7806 (mmm) REVERT: E 119 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7326 (tm-30) REVERT: E 148 SER cc_start: 0.8545 (p) cc_final: 0.8328 (m) REVERT: G 120 THR cc_start: 0.7852 (t) cc_final: 0.7541 (t) outliers start: 41 outliers final: 12 residues processed: 223 average time/residue: 0.6954 time to fit residues: 172.6434 Evaluate side-chains 211 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 109 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 178 optimal weight: 0.0980 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 118 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 467 GLN H 468 ASN A 55 GLN A 865 HIS D 693 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.170545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116126 restraints weight = 24215.862| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.12 r_work: 0.3109 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19449 Z= 0.096 Angle : 0.459 9.357 27008 Z= 0.246 Chirality : 0.036 0.148 3113 Planarity : 0.003 0.026 2835 Dihedral : 19.153 179.575 4451 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.65 % Allowed : 11.27 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.20), residues: 1823 helix: 2.36 (0.19), residues: 801 sheet: 0.17 (0.30), residues: 290 loop : -0.27 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 49 TYR 0.022 0.001 TYR A 249 PHE 0.011 0.001 PHE A 819 TRP 0.012 0.001 TRP A 496 HIS 0.010 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00199 (19445) covalent geometry : angle 0.45604 (27002) hydrogen bonds : bond 0.03831 ( 799) hydrogen bonds : angle 3.88939 ( 2292) metal coordination : bond 0.00485 ( 4) metal coordination : angle 3.34256 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: H 472 GLN cc_start: 0.4333 (tp40) cc_final: 0.3673 (tm130) REVERT: H 490 GLU cc_start: 0.5472 (tp30) cc_final: 0.5187 (tp30) REVERT: H 521 PHE cc_start: 0.5277 (OUTLIER) cc_final: 0.4568 (m-10) REVERT: A 566 MET cc_start: 0.8308 (tpp) cc_final: 0.8036 (mmt) REVERT: A 589 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7805 (p0) REVERT: A 643 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7942 (t70) REVERT: A 848 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7930 (mp-120) REVERT: A 859 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7466 (pm20) REVERT: A 920 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8489 (tt) REVERT: D 588 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7955 (mtm180) REVERT: D 633 ASN cc_start: 0.7240 (m110) cc_final: 0.6659 (t0) REVERT: E 86 MET cc_start: 0.8107 (mmt) cc_final: 0.7604 (mmp) REVERT: E 105 MET cc_start: 0.5123 (pmm) cc_final: 0.3618 (tpt) REVERT: E 119 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7268 (tm-30) REVERT: G 49 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.8035 (ttt-90) REVERT: G 120 THR cc_start: 0.7834 (t) cc_final: 0.7466 (t) outliers start: 44 outliers final: 17 residues processed: 236 average time/residue: 0.6385 time to fit residues: 168.8032 Evaluate side-chains 216 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 21 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 693 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.168141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113016 restraints weight = 23889.261| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.11 r_work: 0.3061 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19449 Z= 0.133 Angle : 0.493 7.352 27008 Z= 0.265 Chirality : 0.037 0.150 3113 Planarity : 0.003 0.026 2835 Dihedral : 19.188 178.838 4451 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.95 % Allowed : 12.65 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.20), residues: 1823 helix: 2.26 (0.19), residues: 803 sheet: 0.15 (0.31), residues: 284 loop : -0.30 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 655 TYR 0.016 0.001 TYR A 490 PHE 0.018 0.001 PHE H 526 TRP 0.014 0.002 TRP A 496 HIS 0.016 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00308 (19445) covalent geometry : angle 0.49024 (27002) hydrogen bonds : bond 0.04686 ( 799) hydrogen bonds : angle 4.01731 ( 2292) metal coordination : bond 0.00673 ( 4) metal coordination : angle 3.68650 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: H 471 GLU cc_start: 0.5326 (OUTLIER) cc_final: 0.4172 (mt-10) REVERT: H 472 GLN cc_start: 0.4139 (tp40) cc_final: 0.3417 (tm130) REVERT: H 479 LEU cc_start: 0.5400 (tt) cc_final: 0.5009 (mt) REVERT: H 490 GLU cc_start: 0.5246 (tp30) cc_final: 0.4975 (tp30) REVERT: H 521 PHE cc_start: 0.5220 (OUTLIER) cc_final: 0.4493 (m-10) REVERT: A 41 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8350 (mp) REVERT: A 566 MET cc_start: 0.8329 (tpp) cc_final: 0.8052 (mmt) REVERT: A 629 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8049 (mmp) REVERT: A 643 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7908 (t70) REVERT: A 848 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7937 (mp-120) REVERT: A 859 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7391 (pm20) REVERT: A 991 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8284 (t0) REVERT: D 588 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7871 (mtm-85) REVERT: D 633 ASN cc_start: 0.7249 (m110) cc_final: 0.6640 (t0) REVERT: E 34 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8359 (pp) REVERT: E 86 MET cc_start: 0.8137 (mmt) cc_final: 0.7635 (mmp) REVERT: E 119 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7352 (tm-30) REVERT: G 120 THR cc_start: 0.7855 (t) cc_final: 0.7479 (t) outliers start: 49 outliers final: 21 residues processed: 230 average time/residue: 0.6521 time to fit residues: 168.3025 Evaluate side-chains 223 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 471 GLU Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 128 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 461 GLN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 482 HIS A 865 HIS D 693 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113788 restraints weight = 23800.810| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.04 r_work: 0.3076 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19449 Z= 0.112 Angle : 0.480 7.922 27008 Z= 0.258 Chirality : 0.037 0.152 3113 Planarity : 0.003 0.040 2835 Dihedral : 19.173 178.744 4451 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.19 % Allowed : 13.19 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.20), residues: 1823 helix: 2.28 (0.19), residues: 801 sheet: 0.21 (0.31), residues: 273 loop : -0.32 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 49 TYR 0.023 0.001 TYR A 249 PHE 0.011 0.001 PHE E 147 TRP 0.014 0.002 TRP A 496 HIS 0.008 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00251 (19445) covalent geometry : angle 0.47724 (27002) hydrogen bonds : bond 0.04326 ( 799) hydrogen bonds : angle 3.95412 ( 2292) metal coordination : bond 0.00539 ( 4) metal coordination : angle 3.74804 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: H 471 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.4291 (mt-10) REVERT: H 472 GLN cc_start: 0.4168 (tp40) cc_final: 0.3387 (tm130) REVERT: H 479 LEU cc_start: 0.5333 (tt) cc_final: 0.4983 (mt) REVERT: H 490 GLU cc_start: 0.5279 (tp30) cc_final: 0.4971 (tp30) REVERT: H 521 PHE cc_start: 0.5246 (OUTLIER) cc_final: 0.4515 (m-10) REVERT: A 41 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8363 (mp) REVERT: A 403 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: A 566 MET cc_start: 0.8318 (tpp) cc_final: 0.8050 (mmt) REVERT: A 629 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8062 (mmp) REVERT: A 643 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7919 (t70) REVERT: A 848 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7980 (mp-120) REVERT: A 991 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8251 (t0) REVERT: D 588 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7964 (mtm-85) REVERT: D 633 ASN cc_start: 0.7262 (m110) cc_final: 0.6632 (t0) REVERT: D 661 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8160 (mt-10) REVERT: E 34 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8320 (pp) REVERT: E 86 MET cc_start: 0.8116 (mmt) cc_final: 0.7616 (mmp) REVERT: E 97 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: E 104 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7068 (ttpp) REVERT: E 119 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7306 (tm-30) REVERT: G 120 THR cc_start: 0.7864 (t) cc_final: 0.7504 (t) outliers start: 53 outliers final: 23 residues processed: 230 average time/residue: 0.6287 time to fit residues: 161.8479 Evaluate side-chains 232 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 471 GLU Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 693 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.168236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.113195 restraints weight = 23923.748| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.09 r_work: 0.3071 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19449 Z= 0.115 Angle : 0.487 7.994 27008 Z= 0.261 Chirality : 0.037 0.152 3113 Planarity : 0.003 0.033 2835 Dihedral : 19.173 178.639 4451 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.89 % Allowed : 13.80 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.20), residues: 1823 helix: 2.26 (0.19), residues: 802 sheet: 0.15 (0.31), residues: 281 loop : -0.30 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 49 TYR 0.015 0.001 TYR A 490 PHE 0.023 0.001 PHE H 526 TRP 0.014 0.002 TRP A 496 HIS 0.021 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00260 (19445) covalent geometry : angle 0.48323 (27002) hydrogen bonds : bond 0.04369 ( 799) hydrogen bonds : angle 3.95650 ( 2292) metal coordination : bond 0.00545 ( 4) metal coordination : angle 3.90278 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: H 472 GLN cc_start: 0.4181 (tp40) cc_final: 0.3355 (tm130) REVERT: H 479 LEU cc_start: 0.5261 (tt) cc_final: 0.4922 (mt) REVERT: H 490 GLU cc_start: 0.5349 (tp30) cc_final: 0.5112 (tp30) REVERT: H 521 PHE cc_start: 0.5269 (OUTLIER) cc_final: 0.4503 (m-10) REVERT: A 31 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8515 (mptt) REVERT: A 41 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8365 (mp) REVERT: A 403 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: A 566 MET cc_start: 0.8296 (tpp) cc_final: 0.8029 (mmt) REVERT: A 629 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8066 (mmp) REVERT: A 643 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7956 (t70) REVERT: A 848 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8000 (mp-120) REVERT: A 991 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8252 (t0) REVERT: D 588 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7948 (mtm-85) REVERT: D 633 ASN cc_start: 0.7291 (m110) cc_final: 0.6639 (t0) REVERT: D 661 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8127 (mt-10) REVERT: E 29 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6254 (tm-30) REVERT: E 34 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8480 (pp) REVERT: E 86 MET cc_start: 0.8125 (mmt) cc_final: 0.7547 (mmp) REVERT: E 88 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7642 (tmtm) REVERT: E 97 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7318 (mm-30) REVERT: E 104 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6996 (ttpp) REVERT: E 105 MET cc_start: 0.5034 (pmm) cc_final: 0.3337 (tpp) REVERT: E 119 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7301 (tm-30) REVERT: G 120 THR cc_start: 0.7827 (t) cc_final: 0.7459 (t) REVERT: G 153 LYS cc_start: 0.8579 (pttm) cc_final: 0.8342 (pttp) outliers start: 48 outliers final: 26 residues processed: 228 average time/residue: 0.6449 time to fit residues: 164.8317 Evaluate side-chains 235 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 24 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 73 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 102 optimal weight: 0.0040 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 overall best weight: 0.2428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 77 GLN A 865 HIS D 693 HIS F 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.170900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116521 restraints weight = 24034.372| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.07 r_work: 0.3126 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19449 Z= 0.091 Angle : 0.459 8.233 27008 Z= 0.247 Chirality : 0.036 0.145 3113 Planarity : 0.003 0.033 2835 Dihedral : 19.120 179.981 4451 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.23 % Allowed : 14.64 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.20), residues: 1823 helix: 2.36 (0.19), residues: 805 sheet: 0.12 (0.30), residues: 287 loop : -0.22 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 49 TYR 0.025 0.001 TYR A 249 PHE 0.013 0.001 PHE D 657 TRP 0.013 0.001 TRP A 496 HIS 0.034 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00186 (19445) covalent geometry : angle 0.45619 (27002) hydrogen bonds : bond 0.03622 ( 799) hydrogen bonds : angle 3.81216 ( 2292) metal coordination : bond 0.00377 ( 4) metal coordination : angle 3.55394 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.611 Fit side-chains REVERT: H 471 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.4586 (mt-10) REVERT: H 472 GLN cc_start: 0.4187 (tp40) cc_final: 0.3361 (tm130) REVERT: H 479 LEU cc_start: 0.5270 (tt) cc_final: 0.4929 (mt) REVERT: H 521 PHE cc_start: 0.5311 (OUTLIER) cc_final: 0.4525 (m-10) REVERT: H 531 GLN cc_start: 0.3535 (mt0) cc_final: 0.3002 (mp10) REVERT: A 31 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8430 (mptt) REVERT: A 403 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: A 629 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8011 (mmp) REVERT: A 643 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7920 (t70) REVERT: A 848 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8023 (mp-120) REVERT: A 920 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8537 (tt) REVERT: D 588 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7862 (mtm-85) REVERT: D 633 ASN cc_start: 0.7254 (m110) cc_final: 0.6624 (t0) REVERT: D 661 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8140 (mt-10) REVERT: E 29 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6382 (tm-30) REVERT: E 86 MET cc_start: 0.8102 (mmt) cc_final: 0.7531 (mmp) REVERT: E 88 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7561 (tmtm) REVERT: E 104 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6876 (ttpp) REVERT: E 119 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7282 (tm-30) REVERT: F 73 ILE cc_start: 0.8009 (pt) cc_final: 0.7338 (mt) REVERT: G 87 ASP cc_start: 0.8551 (p0) cc_final: 0.8181 (p0) REVERT: G 120 THR cc_start: 0.7764 (t) cc_final: 0.7386 (t) REVERT: G 153 LYS cc_start: 0.8586 (pttm) cc_final: 0.8364 (pttp) outliers start: 37 outliers final: 14 residues processed: 222 average time/residue: 0.6258 time to fit residues: 155.9986 Evaluate side-chains 218 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 471 GLU Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 122 optimal weight: 0.9990 chunk 155 optimal weight: 0.0370 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 440 GLN A 444 GLN A 865 HIS D 619 HIS D 693 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.169434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114488 restraints weight = 23885.278| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.08 r_work: 0.3089 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 19449 Z= 0.109 Angle : 0.480 8.281 27008 Z= 0.258 Chirality : 0.036 0.148 3113 Planarity : 0.003 0.040 2835 Dihedral : 19.124 179.750 4451 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.93 % Allowed : 15.30 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.20), residues: 1823 helix: 2.31 (0.19), residues: 808 sheet: 0.21 (0.31), residues: 271 loop : -0.27 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 49 TYR 0.014 0.001 TYR A 490 PHE 0.027 0.001 PHE H 526 TRP 0.014 0.002 TRP A 496 HIS 0.008 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00244 (19445) covalent geometry : angle 0.47738 (27002) hydrogen bonds : bond 0.04079 ( 799) hydrogen bonds : angle 3.86692 ( 2292) metal coordination : bond 0.00462 ( 4) metal coordination : angle 3.65764 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.614 Fit side-chains REVERT: H 471 GLU cc_start: 0.5079 (mp0) cc_final: 0.4571 (mt-10) REVERT: H 472 GLN cc_start: 0.4147 (tp40) cc_final: 0.3269 (tm130) REVERT: H 479 LEU cc_start: 0.5269 (tt) cc_final: 0.4921 (mt) REVERT: H 521 PHE cc_start: 0.5381 (OUTLIER) cc_final: 0.4621 (m-10) REVERT: A 31 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8447 (mptt) REVERT: A 403 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: A 629 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8072 (mmp) REVERT: A 643 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7941 (t70) REVERT: A 848 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7931 (mp-120) REVERT: D 588 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7889 (mtm-85) REVERT: D 633 ASN cc_start: 0.7230 (m110) cc_final: 0.6574 (t0) REVERT: D 661 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8148 (mt-10) REVERT: D 664 ASN cc_start: 0.7304 (t0) cc_final: 0.7075 (t160) REVERT: E 29 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6418 (tm-30) REVERT: E 86 MET cc_start: 0.8104 (mmt) cc_final: 0.7501 (mmp) REVERT: E 88 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7616 (tmtm) REVERT: E 119 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7343 (tm-30) REVERT: F 73 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7384 (mt) REVERT: G 87 ASP cc_start: 0.8567 (p0) cc_final: 0.8207 (p0) REVERT: G 120 THR cc_start: 0.7769 (t) cc_final: 0.7398 (t) REVERT: G 153 LYS cc_start: 0.8540 (pttm) cc_final: 0.8338 (pttp) outliers start: 32 outliers final: 17 residues processed: 206 average time/residue: 0.6194 time to fit residues: 143.1160 Evaluate side-chains 217 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 102 optimal weight: 0.0470 chunk 94 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 461 GLN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 693 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.169533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115533 restraints weight = 23897.920| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.91 r_work: 0.3108 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19449 Z= 0.107 Angle : 0.484 9.543 27008 Z= 0.259 Chirality : 0.036 0.147 3113 Planarity : 0.003 0.041 2835 Dihedral : 19.120 179.474 4451 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.99 % Allowed : 15.12 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.41 (0.20), residues: 1823 helix: 2.30 (0.19), residues: 808 sheet: 0.18 (0.31), residues: 271 loop : -0.26 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 49 TYR 0.025 0.001 TYR A 249 PHE 0.013 0.001 PHE H 525 TRP 0.013 0.002 TRP A 496 HIS 0.015 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00239 (19445) covalent geometry : angle 0.48095 (27002) hydrogen bonds : bond 0.04062 ( 799) hydrogen bonds : angle 3.87969 ( 2292) metal coordination : bond 0.00433 ( 4) metal coordination : angle 3.63688 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.589 Fit side-chains REVERT: H 471 GLU cc_start: 0.5224 (OUTLIER) cc_final: 0.4719 (mt-10) REVERT: H 472 GLN cc_start: 0.4123 (tp40) cc_final: 0.3258 (tm130) REVERT: H 479 LEU cc_start: 0.5284 (tt) cc_final: 0.4919 (mt) REVERT: H 512 ASN cc_start: 0.5795 (t0) cc_final: 0.5505 (t0) REVERT: H 521 PHE cc_start: 0.5456 (OUTLIER) cc_final: 0.4703 (m-10) REVERT: H 531 GLN cc_start: 0.3634 (mt0) cc_final: 0.3087 (mp10) REVERT: A 31 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8448 (mptt) REVERT: A 629 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8033 (mmp) REVERT: A 643 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7916 (t70) REVERT: A 848 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7938 (mp-120) REVERT: A 920 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8534 (tt) REVERT: A 991 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8181 (t0) REVERT: D 588 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7904 (mtm-85) REVERT: D 633 ASN cc_start: 0.7246 (m110) cc_final: 0.6590 (t0) REVERT: D 661 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8129 (mt-10) REVERT: E 29 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: E 86 MET cc_start: 0.8100 (mmt) cc_final: 0.7499 (mmp) REVERT: E 88 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7577 (tmtm) REVERT: E 105 MET cc_start: 0.4918 (pmm) cc_final: 0.3359 (tpt) REVERT: E 119 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 73 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7403 (mt) REVERT: G 87 ASP cc_start: 0.8565 (p0) cc_final: 0.8203 (p0) REVERT: G 120 THR cc_start: 0.7785 (t) cc_final: 0.7411 (t) REVERT: G 153 LYS cc_start: 0.8540 (pttm) cc_final: 0.8302 (ptmt) outliers start: 33 outliers final: 18 residues processed: 210 average time/residue: 0.6334 time to fit residues: 149.3078 Evaluate side-chains 220 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 471 GLU Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 142 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 196 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 664 ASN D 693 HIS F 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.168908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113688 restraints weight = 24012.742| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.09 r_work: 0.3076 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19449 Z= 0.125 Angle : 0.501 9.299 27008 Z= 0.268 Chirality : 0.037 0.149 3113 Planarity : 0.003 0.040 2835 Dihedral : 19.138 178.725 4451 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.87 % Allowed : 15.42 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.20), residues: 1823 helix: 2.25 (0.19), residues: 808 sheet: 0.18 (0.31), residues: 271 loop : -0.29 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 49 TYR 0.015 0.001 TYR A 150 PHE 0.018 0.001 PHE H 526 TRP 0.013 0.002 TRP A 496 HIS 0.018 0.001 HIS D 693 Details of bonding type rmsd covalent geometry : bond 0.00287 (19445) covalent geometry : angle 0.49736 (27002) hydrogen bonds : bond 0.04407 ( 799) hydrogen bonds : angle 3.94887 ( 2292) metal coordination : bond 0.00516 ( 4) metal coordination : angle 3.86665 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7500.85 seconds wall clock time: 128 minutes 20.45 seconds (7700.45 seconds total)