Starting phenix.real_space_refine on Mon Sep 14 00:13:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pkw_20368/09_2026/6pkw_20368.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pkw_20368/09_2026/6pkw_20368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pkw_20368/09_2026/6pkw_20368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pkw_20368/09_2026/6pkw_20368.map" model { file = "/net/cci-nas-00/data/ceres_data/6pkw_20368/09_2026/6pkw_20368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pkw_20368/09_2026/6pkw_20368.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 16710 2.51 5 N 4758 2.21 5 O 4742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26262 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 885, 5649 Classifications: {'peptide': 885} Incomplete info: {'truncation_to_alanine': 446} Link IDs: {'PTRANS': 22, 'TRANS': 862} Chain breaks: 14 Unresolved non-hydrogen bonds: 1625 Unresolved non-hydrogen angles: 2047 Unresolved non-hydrogen dihedrals: 1301 Unresolved non-hydrogen chiralities: 159 Planarities with less than four sites: {'GLU:plan': 59, 'ARG:plan': 39, 'ASP:plan': 30, 'ASN:plan1': 19, 'GLN:plan1': 22, 'TYR:plan': 14, 'HIS:plan': 5, 'PHE:plan': 16, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 903 Chain: "A" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1306 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 8 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'UNK:plan-1': 22, 'ASP:plan': 5, 'GLU:plan': 6, 'HIS:plan': 3, 'ARG:plan': 11, 'GLN:plan1': 6, 'ASN:plan1': 6, 'TYR:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 205 Chain: "B" Number of atoms: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 4872 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 436} Link IDs: {'PTRANS': 20, 'TRANS': 764} Chain breaks: 20 Unresolved non-hydrogen bonds: 1634 Unresolved non-hydrogen angles: 2070 Unresolved non-hydrogen dihedrals: 1326 Unresolved non-hydrogen chiralities: 163 Planarities with less than four sites: {'GLU:plan': 54, 'ARG:plan': 35, 'ASP:plan': 28, 'GLN:plan1': 22, 'HIS:plan': 9, 'TYR:plan': 11, 'ASN:plan1': 16, 'PHE:plan': 21, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 904 Chain: "B" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1304 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 8 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'UNK:plan-1': 22, 'ASP:plan': 5, 'GLU:plan': 6, 'HIS:plan': 3, 'ARG:plan': 11, 'GLN:plan1': 6, 'ASN:plan1': 6, 'TYR:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 205 Restraints were copied for chains: C, D Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N GLU A1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A1272 " occ=0.50 residue: pdb=" N VAL A1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL A1287 " occ=0.50 residue: pdb=" N VAL A1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL A1400 " occ=0.50 residue: pdb=" N GLU C1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C1272 " occ=0.50 residue: pdb=" N VAL C1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL C1287 " occ=0.50 residue: pdb=" N VAL C1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL C1400 " occ=0.50 residue: pdb=" N GLU B1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B1272 " occ=0.50 residue: pdb=" N VAL B1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL B1287 " occ=0.50 residue: pdb=" N VAL B1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL B1400 " occ=0.50 residue: pdb=" N GLU D1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU D1272 " occ=0.50 residue: pdb=" N VAL D1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL D1287 " occ=0.50 residue: pdb=" N VAL D1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D1400 " occ=0.50 Time building chain proxies: 12.21, per 1000 atoms: 0.46 Number of scatterers: 26262 At special positions: 0 Unit cell: (148.174, 146.042, 178.022, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 4742 8.00 N 4758 7.00 C 16710 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: 2.02 Conformation dependent library (CDL) restraints added in 918.5 milliseconds 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7916 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 14 sheets defined 68.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.916A pdb=" N THR A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 removed outlier: 3.838A pdb=" N HIS A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.762A pdb=" N ASN A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 406 through 419 Processing helix chain 'A' and resid 426 through 439 removed outlier: 4.075A pdb=" N ALA A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.837A pdb=" N ALA A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 470 removed outlier: 4.116A pdb=" N GLY A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 3.605A pdb=" N ARG A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.974A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 536 through 548 Processing helix chain 'A' and resid 593 through 605 removed outlier: 3.587A pdb=" N GLN A 605 " --> pdb=" O TRP A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.763A pdb=" N ALA A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 639 removed outlier: 3.579A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 672 removed outlier: 3.558A pdb=" N LEU A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.514A pdb=" N ALA A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 720 Processing helix chain 'A' and resid 729 through 737 Processing helix chain 'A' and resid 738 through 742 removed outlier: 4.157A pdb=" N ILE A 741 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 762 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 808 through 834 removed outlier: 3.634A pdb=" N ASP A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 864 removed outlier: 3.686A pdb=" N HIS A 863 " --> pdb=" O ARG A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 Processing helix chain 'A' and resid 880 through 902 Processing helix chain 'A' and resid 904 through 926 removed outlier: 3.932A pdb=" N ILE A 920 " --> pdb=" O CYS A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 929 No H-bonds generated for 'chain 'A' and resid 927 through 929' Processing helix chain 'A' and resid 935 through 949 removed outlier: 4.033A pdb=" N LYS A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 947 " --> pdb=" O VAL A 943 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP A 949 " --> pdb=" O ARG A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 972 Processing helix chain 'A' and resid 978 through 995 removed outlier: 5.456A pdb=" N GLU A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Proline residue: A 990 - end of helix Processing helix chain 'A' and resid 1036 through 1065 removed outlier: 3.592A pdb=" N THR A1040 " --> pdb=" O PRO A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1092 removed outlier: 3.570A pdb=" N ILE A1077 " --> pdb=" O ASN A1073 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A1083 " --> pdb=" O LYS A1079 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1114 removed outlier: 4.150A pdb=" N LEU A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1156 removed outlier: 3.758A pdb=" N SER A1156 " --> pdb=" O ARG A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1184 Processing helix chain 'A' and resid 1189 through 1206 Processing helix chain 'A' and resid 1370 through 1381 removed outlier: 3.594A pdb=" N LEU A1381 " --> pdb=" O LEU A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1432 Processing helix chain 'A' and resid 1456 through 1467 removed outlier: 3.545A pdb=" N ARG A1460 " --> pdb=" O CYS A1456 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 48 Processing helix chain 'C' and resid 126 through 136 Processing helix chain 'C' and resid 159 through 178 removed outlier: 3.917A pdb=" N THR C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 removed outlier: 3.839A pdb=" N HIS C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.762A pdb=" N ASN C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 354 through 363 Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 406 through 419 Processing helix chain 'C' and resid 426 through 439 removed outlier: 4.074A pdb=" N ALA C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 448 removed outlier: 3.838A pdb=" N ALA C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 470 removed outlier: 4.117A pdb=" N GLY C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.605A pdb=" N ARG C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 490 Processing helix chain 'C' and resid 492 through 502 removed outlier: 3.975A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 517 Processing helix chain 'C' and resid 536 through 548 Processing helix chain 'C' and resid 593 through 605 removed outlier: 3.587A pdb=" N GLN C 605 " --> pdb=" O TRP C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 618 removed outlier: 3.763A pdb=" N ALA C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 639 removed outlier: 3.579A pdb=" N GLU C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 672 removed outlier: 3.558A pdb=" N LEU C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 682 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 701 through 706 removed outlier: 3.514A pdb=" N ALA C 706 " --> pdb=" O LYS C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 720 Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'C' and resid 738 through 742 removed outlier: 4.156A pdb=" N ILE C 741 " --> pdb=" O PHE C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 808 through 834 removed outlier: 3.634A pdb=" N ASP C 834 " --> pdb=" O VAL C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 864 removed outlier: 3.686A pdb=" N HIS C 863 " --> pdb=" O ARG C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 880 Processing helix chain 'C' and resid 880 through 902 Processing helix chain 'C' and resid 904 through 926 removed outlier: 3.932A pdb=" N ILE C 920 " --> pdb=" O CYS C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 929 No H-bonds generated for 'chain 'C' and resid 927 through 929' Processing helix chain 'C' and resid 935 through 949 removed outlier: 4.033A pdb=" N LYS C 939 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 947 " --> pdb=" O VAL C 943 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 972 Processing helix chain 'C' and resid 978 through 995 removed outlier: 5.456A pdb=" N GLU C 989 " --> pdb=" O GLY C 985 " (cutoff:3.500A) Proline residue: C 990 - end of helix Processing helix chain 'C' and resid 1036 through 1065 removed outlier: 3.592A pdb=" N THR C1040 " --> pdb=" O PRO C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1092 removed outlier: 3.570A pdb=" N ILE C1077 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR C1083 " --> pdb=" O LYS C1079 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU C1084 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1096 through 1114 removed outlier: 4.149A pdb=" N LEU C1102 " --> pdb=" O PRO C1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1156 removed outlier: 3.758A pdb=" N SER C1156 " --> pdb=" O ARG C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1184 Processing helix chain 'C' and resid 1189 through 1206 Processing helix chain 'C' and resid 1370 through 1381 removed outlier: 3.593A pdb=" N LEU C1381 " --> pdb=" O LEU C1377 " (cutoff:3.500A) Processing helix chain 'C' and resid 1428 through 1432 Processing helix chain 'C' and resid 1456 through 1467 removed outlier: 3.546A pdb=" N ARG C1460 " --> pdb=" O CYS C1456 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.704A pdb=" N ASN B 47 " --> pdb=" O TRP B 43 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.557A pdb=" N LEU B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 190 through 201 removed outlier: 3.734A pdb=" N VAL B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 407 through 421 Processing helix chain 'B' and resid 427 through 439 removed outlier: 3.850A pdb=" N ALA B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 Processing helix chain 'B' and resid 456 through 459 removed outlier: 3.574A pdb=" N ASP B 459 " --> pdb=" O THR B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 459' Processing helix chain 'B' and resid 460 through 469 Processing helix chain 'B' and resid 472 through 483 removed outlier: 3.565A pdb=" N ARG B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.623A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.923A pdb=" N GLN B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 548 Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 607 through 618 Processing helix chain 'B' and resid 620 through 638 Processing helix chain 'B' and resid 648 through 672 removed outlier: 3.706A pdb=" N VAL B 664 " --> pdb=" O GLN B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 681 Processing helix chain 'B' and resid 691 through 700 Processing helix chain 'B' and resid 701 through 706 removed outlier: 3.837A pdb=" N ILE B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 720 Processing helix chain 'B' and resid 729 through 737 Processing helix chain 'B' and resid 738 through 743 removed outlier: 4.151A pdb=" N ILE B 741 " --> pdb=" O PHE B 738 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 742 " --> pdb=" O PRO B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 762 Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 808 through 832 removed outlier: 4.532A pdb=" N MET B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 862 Processing helix chain 'B' and resid 870 through 880 Processing helix chain 'B' and resid 881 through 902 Processing helix chain 'B' and resid 904 through 932 removed outlier: 4.177A pdb=" N LEU B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 925 " --> pdb=" O ILE B 921 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 929 " --> pdb=" O ARG B 925 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE B 930 " --> pdb=" O LEU B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 941 removed outlier: 3.527A pdb=" N LYS B 939 " --> pdb=" O THR B 935 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 949 removed outlier: 4.440A pdb=" N MET B 946 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET B 947 " --> pdb=" O VAL B 943 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU B 948 " --> pdb=" O ARG B 944 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP B 949 " --> pdb=" O ARG B 945 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 942 through 949' Processing helix chain 'B' and resid 949 through 972 Processing helix chain 'B' and resid 979 through 995 removed outlier: 3.649A pdb=" N ILE B 983 " --> pdb=" O LEU B 979 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU B 989 " --> pdb=" O GLY B 985 " (cutoff:3.500A) Proline residue: B 990 - end of helix removed outlier: 3.532A pdb=" N ILE B 994 " --> pdb=" O PRO B 990 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 995 " --> pdb=" O TYR B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1065 Processing helix chain 'B' and resid 1073 through 1092 removed outlier: 3.865A pdb=" N TYR B1083 " --> pdb=" O LYS B1079 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU B1084 " --> pdb=" O PHE B1080 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1114 removed outlier: 4.452A pdb=" N LEU B1102 " --> pdb=" O PRO B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1156 Processing helix chain 'B' and resid 1158 through 1184 Processing helix chain 'B' and resid 1189 through 1207 Processing helix chain 'B' and resid 1270 through 1275 Processing helix chain 'B' and resid 1370 through 1381 Processing helix chain 'B' and resid 1456 through 1467 Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.703A pdb=" N ASN D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 48 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 137 removed outlier: 3.557A pdb=" N LEU D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 175 Processing helix chain 'D' and resid 190 through 201 removed outlier: 3.734A pdb=" N VAL D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 407 through 421 Processing helix chain 'D' and resid 427 through 439 removed outlier: 3.850A pdb=" N ALA D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 449 Processing helix chain 'D' and resid 456 through 459 removed outlier: 3.573A pdb=" N ASP D 459 " --> pdb=" O THR D 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 456 through 459' Processing helix chain 'D' and resid 460 through 469 Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.565A pdb=" N ARG D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 490 Processing helix chain 'D' and resid 492 through 502 removed outlier: 3.622A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 517 removed outlier: 3.922A pdb=" N GLN D 517 " --> pdb=" O ALA D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 548 Processing helix chain 'D' and resid 593 through 606 Processing helix chain 'D' and resid 607 through 618 Processing helix chain 'D' and resid 620 through 638 Processing helix chain 'D' and resid 648 through 672 removed outlier: 3.706A pdb=" N VAL D 664 " --> pdb=" O GLN D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 681 Processing helix chain 'D' and resid 691 through 700 Processing helix chain 'D' and resid 701 through 706 removed outlier: 3.837A pdb=" N ILE D 705 " --> pdb=" O ASP D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 720 Processing helix chain 'D' and resid 729 through 737 Processing helix chain 'D' and resid 738 through 743 removed outlier: 4.150A pdb=" N ILE D 741 " --> pdb=" O PHE D 738 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 742 " --> pdb=" O PRO D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 762 Processing helix chain 'D' and resid 799 through 807 Processing helix chain 'D' and resid 808 through 832 removed outlier: 4.532A pdb=" N MET D 832 " --> pdb=" O ALA D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 862 Processing helix chain 'D' and resid 870 through 880 Processing helix chain 'D' and resid 881 through 902 Processing helix chain 'D' and resid 904 through 932 removed outlier: 4.176A pdb=" N LEU D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG D 925 " --> pdb=" O ILE D 921 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 929 " --> pdb=" O ARG D 925 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE D 930 " --> pdb=" O LEU D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 935 through 941 removed outlier: 3.527A pdb=" N LYS D 939 " --> pdb=" O THR D 935 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 949 removed outlier: 4.440A pdb=" N MET D 946 " --> pdb=" O ILE D 942 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET D 947 " --> pdb=" O VAL D 943 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU D 948 " --> pdb=" O ARG D 944 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP D 949 " --> pdb=" O ARG D 945 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 942 through 949' Processing helix chain 'D' and resid 949 through 972 Processing helix chain 'D' and resid 979 through 995 removed outlier: 3.650A pdb=" N ILE D 983 " --> pdb=" O LEU D 979 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU D 989 " --> pdb=" O GLY D 985 " (cutoff:3.500A) Proline residue: D 990 - end of helix removed outlier: 3.532A pdb=" N ILE D 994 " --> pdb=" O PRO D 990 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 995 " --> pdb=" O TYR D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1065 Processing helix chain 'D' and resid 1073 through 1092 removed outlier: 3.865A pdb=" N TYR D1083 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU D1084 " --> pdb=" O PHE D1080 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1114 removed outlier: 4.452A pdb=" N LEU D1102 " --> pdb=" O PRO D1098 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1156 Processing helix chain 'D' and resid 1158 through 1184 Processing helix chain 'D' and resid 1189 through 1207 Processing helix chain 'D' and resid 1270 through 1275 Processing helix chain 'D' and resid 1370 through 1381 Processing helix chain 'D' and resid 1456 through 1467 Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 122 removed outlier: 6.063A pdb=" N ILE A 181 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL A 217 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 183 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 147 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N GLY A 184 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N VAL A 149 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 146 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL A 304 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SER A 148 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL A 327 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 683 through 684 removed outlier: 3.531A pdb=" N SER A 684 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER A 690 " --> pdb=" O SER A 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 5.539A pdb=" N GLY A1323 " --> pdb=" O TRP A1410 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU A1412 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASN A1325 " --> pdb=" O GLU A1412 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N SER A1414 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A1327 " --> pdb=" O SER A1414 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE A1416 " --> pdb=" O ILE A1327 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS A1329 " --> pdb=" O ILE A1416 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A1418 " --> pdb=" O HIS A1329 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE A1331 " --> pdb=" O LEU A1418 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL A1411 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N TYR A1399 " --> pdb=" O VAL A1411 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A1413 " --> pdb=" O LYS A1397 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS A1397 " --> pdb=" O THR A1413 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A1415 " --> pdb=" O VAL A1395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 6.145A pdb=" N PHE A1332 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1346 " --> pdb=" O PHE A1332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 117 through 122 removed outlier: 6.063A pdb=" N ILE C 181 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL C 217 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C 183 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE C 147 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N GLY C 184 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL C 149 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 146 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL C 304 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER C 148 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL C 327 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 683 through 684 removed outlier: 3.531A pdb=" N SER C 684 " --> pdb=" O SER C 690 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER C 690 " --> pdb=" O SER C 684 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 5.539A pdb=" N GLY C1323 " --> pdb=" O TRP C1410 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU C1412 " --> pdb=" O GLY C1323 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASN C1325 " --> pdb=" O GLU C1412 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER C1414 " --> pdb=" O ASN C1325 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C1327 " --> pdb=" O SER C1414 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE C1416 " --> pdb=" O ILE C1327 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS C1329 " --> pdb=" O ILE C1416 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU C1418 " --> pdb=" O HIS C1329 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE C1331 " --> pdb=" O LEU C1418 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N VAL C1411 " --> pdb=" O TYR C1399 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR C1399 " --> pdb=" O VAL C1411 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR C1413 " --> pdb=" O LYS C1397 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS C1397 " --> pdb=" O THR C1413 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C1415 " --> pdb=" O VAL C1395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 6.145A pdb=" N PHE C1332 " --> pdb=" O LEU C1346 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C1346 " --> pdb=" O PHE C1332 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 121 Processing sheet with id=AB1, first strand: chain 'B' and resid 1361 through 1362 removed outlier: 5.708A pdb=" N GLY B1323 " --> pdb=" O TRP B1410 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU B1412 " --> pdb=" O GLY B1323 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASN B1325 " --> pdb=" O GLU B1412 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N SER B1414 " --> pdb=" O ASN B1325 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B1327 " --> pdb=" O SER B1414 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE B1416 " --> pdb=" O ILE B1327 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS B1329 " --> pdb=" O ILE B1416 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU B1418 " --> pdb=" O HIS B1329 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE B1331 " --> pdb=" O LEU B1418 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N VAL B1411 " --> pdb=" O TYR B1399 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR B1399 " --> pdb=" O VAL B1411 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B1413 " --> pdb=" O LYS B1397 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B1397 " --> pdb=" O THR B1413 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B1415 " --> pdb=" O VAL B1395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1361 through 1362 removed outlier: 6.760A pdb=" N PHE B1332 " --> pdb=" O LEU B1346 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B1346 " --> pdb=" O PHE B1332 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 118 through 121 Processing sheet with id=AB4, first strand: chain 'D' and resid 1361 through 1362 removed outlier: 5.708A pdb=" N GLY D1323 " --> pdb=" O TRP D1410 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU D1412 " --> pdb=" O GLY D1323 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASN D1325 " --> pdb=" O GLU D1412 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N SER D1414 " --> pdb=" O ASN D1325 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE D1327 " --> pdb=" O SER D1414 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE D1416 " --> pdb=" O ILE D1327 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS D1329 " --> pdb=" O ILE D1416 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU D1418 " --> pdb=" O HIS D1329 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE D1331 " --> pdb=" O LEU D1418 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N VAL D1411 " --> pdb=" O TYR D1399 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N TYR D1399 " --> pdb=" O VAL D1411 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR D1413 " --> pdb=" O LYS D1397 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS D1397 " --> pdb=" O THR D1413 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE D1415 " --> pdb=" O VAL D1395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1361 through 1362 removed outlier: 6.760A pdb=" N PHE D1332 " --> pdb=" O LEU D1346 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU D1346 " --> pdb=" O PHE D1332 " (cutoff:3.500A) 1937 hydrogen bonds defined for protein. 5751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8821 1.34 - 1.46: 5155 1.46 - 1.57: 12710 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 26748 Sorted by residual: bond pdb=" C PHE A 738 " pdb=" N PRO A 739 " ideal model delta sigma weight residual 1.334 1.373 -0.040 8.40e-03 1.42e+04 2.24e+01 bond pdb=" C PHE C 738 " pdb=" N PRO C 739 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.16e+01 bond pdb=" C SER B1281 " pdb=" N PRO B1282 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 1.01e+01 bond pdb=" C SER D1281 " pdb=" N PRO D1282 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 1.01e+01 bond pdb=" C SER C1281 " pdb=" N PRO C1282 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 6.94e+00 ... (remaining 26743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 36010 2.72 - 5.44: 711 5.44 - 8.16: 81 8.16 - 10.87: 12 10.87 - 13.59: 8 Bond angle restraints: 36822 Sorted by residual: angle pdb=" N CYS A 621 " pdb=" CA CYS A 621 " pdb=" C CYS A 621 " ideal model delta sigma weight residual 111.28 120.61 -9.33 1.09e+00 8.42e-01 7.32e+01 angle pdb=" N CYS C 621 " pdb=" CA CYS C 621 " pdb=" C CYS C 621 " ideal model delta sigma weight residual 111.28 120.57 -9.29 1.09e+00 8.42e-01 7.26e+01 angle pdb=" N PRO C 504 " pdb=" CA PRO C 504 " pdb=" C PRO C 504 " ideal model delta sigma weight residual 112.47 124.37 -11.90 2.06e+00 2.36e-01 3.33e+01 angle pdb=" N PRO A 504 " pdb=" CA PRO A 504 " pdb=" C PRO A 504 " ideal model delta sigma weight residual 112.47 124.34 -11.87 2.06e+00 2.36e-01 3.32e+01 angle pdb=" N PRO D1097 " pdb=" CA PRO D1097 " pdb=" C PRO D1097 " ideal model delta sigma weight residual 110.70 116.36 -5.66 1.22e+00 6.72e-01 2.15e+01 ... (remaining 36817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.50: 14035 11.50 - 23.01: 1022 23.01 - 34.51: 185 34.51 - 46.02: 40 46.02 - 57.52: 6 Dihedral angle restraints: 15288 sinusoidal: 3266 harmonic: 12022 Sorted by residual: dihedral pdb=" CA ILE C 255 " pdb=" C ILE C 255 " pdb=" N ASN C 256 " pdb=" CA ASN C 256 " ideal model delta harmonic sigma weight residual -180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ILE A 255 " pdb=" C ILE A 255 " pdb=" N ASN A 256 " pdb=" CA ASN A 256 " ideal model delta harmonic sigma weight residual -180.00 -150.17 -29.83 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA PRO D1260 " pdb=" C PRO D1260 " pdb=" N ASP D1261 " pdb=" CA ASP D1261 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 15285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3978 0.076 - 0.152: 474 0.152 - 0.227: 58 0.227 - 0.303: 8 0.303 - 0.379: 2 Chirality restraints: 4520 Sorted by residual: chirality pdb=" CA PRO A 504 " pdb=" N PRO A 504 " pdb=" C PRO A 504 " pdb=" CB PRO A 504 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA PRO C 504 " pdb=" N PRO C 504 " pdb=" C PRO C 504 " pdb=" CB PRO C 504 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB VAL D 302 " pdb=" CA VAL D 302 " pdb=" CG1 VAL D 302 " pdb=" CG2 VAL D 302 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 4517 not shown) Planarity restraints: 4802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 503 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C LEU C 503 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU C 503 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO C 504 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 503 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C LEU A 503 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU A 503 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO A 504 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 592 " 0.022 2.00e-02 2.50e+03 1.82e-02 8.32e+00 pdb=" CG TRP B 592 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 592 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 592 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 592 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 592 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 592 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 592 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 592 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 592 " 0.001 2.00e-02 2.50e+03 ... (remaining 4799 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5705 2.77 - 3.30: 25742 3.30 - 3.84: 43578 3.84 - 4.37: 43563 4.37 - 4.90: 72022 Nonbonded interactions: 190610 Sorted by model distance: nonbonded pdb=" OH TYR B1259 " pdb=" O VAL B1264 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR D1259 " pdb=" O VAL D1264 " model vdw 2.239 3.040 nonbonded pdb=" O VAL C 301 " pdb=" OG1 THR C 324 " model vdw 2.249 3.040 nonbonded pdb=" O VAL A 301 " pdb=" OG1 THR A 324 " model vdw 2.249 3.040 nonbonded pdb=" O ASN D1073 " pdb=" OG1 THR D1076 " model vdw 2.271 3.040 ... (remaining 190605 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.180 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.007 0.074 26748 Z= 0.347 Angle : 0.940 13.592 36822 Z= 0.535 Chirality : 0.052 0.379 4520 Planarity : 0.007 0.062 4802 Dihedral : 9.190 57.520 7372 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -3.48 (0.11), residues: 3848 helix: -1.74 (0.08), residues: 2424 sheet: -2.28 (0.32), residues: 216 loop : -3.23 (0.14), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1310 TYR 0.032 0.003 TYR D 131 PHE 0.023 0.003 PHE C1280 TRP 0.050 0.003 TRP B 592 HIS 0.012 0.003 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.35 (26748) covalent geometry : angle 0.93960 / 0.53 (36822) hydrogen bonds : bond 0.13768 / 9.83 ( 1929) hydrogen bonds : angle 6.62785 / 4.90 ( 5751) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9507 (tp) cc_final: 0.9100 (tt) REVERT: A 438 TRP cc_start: 0.9143 (m-10) cc_final: 0.8616 (m-10) REVERT: A 499 LEU cc_start: 0.9707 (mt) cc_final: 0.9374 (tp) REVERT: A 651 LEU cc_start: 0.9637 (mt) cc_final: 0.9318 (mp) REVERT: A 662 ILE cc_start: 0.9762 (pt) cc_final: 0.9505 (mt) REVERT: A 876 MET cc_start: 0.8593 (mtm) cc_final: 0.8067 (tmm) REVERT: A 1143 MET cc_start: 0.9445 (mmt) cc_final: 0.8899 (mmp) REVERT: A 1429 ASP cc_start: 0.3817 (t0) cc_final: 0.3073 (p0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0705 time to fit residues: 8.6383 Evaluate side-chains 44 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.163 Evaluate side-chains 69 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: B 687 TRP cc_start: 0.8976 (m100) cc_final: 0.8557 (m100) REVERT: B 711 GLN cc_start: 0.9501 (mm-40) cc_final: 0.9207 (mm110) REVERT: B 805 PHE cc_start: 0.9423 (t80) cc_final: 0.9127 (m-80) REVERT: B 1143 MET cc_start: 0.9681 (mmt) cc_final: 0.9385 (mmm) REVERT: B 1169 LYS cc_start: 0.9605 (mttt) cc_final: 0.9401 (tttt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0397 time to fit residues: 4.2318 Evaluate side-chains 45 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 50.0000 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 50.0000 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 0.6980 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 656 HIS A 707 HIS A1081 GLN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 HIS B1164 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.045917 restraints weight = 56198.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.046912 restraints weight = 32914.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.047594 restraints weight = 23017.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.047969 restraints weight = 18000.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.048263 restraints weight = 15347.507| |-----------------------------------------------------------------------------| r_work (final): 0.2841 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.079921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.059061 restraints weight = 56102.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.059038 restraints weight = 37585.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059514 restraints weight = 27843.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059664 restraints weight = 21577.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059604 restraints weight = 21006.897| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 13 (18 function evaluations) r_final: 0.2835 r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (17 function evaluations) r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26748 Z= 0.111 Angle : 0.511 8.610 36822 Z= 0.279 Chirality : 0.037 0.150 4520 Planarity : 0.004 0.053 4802 Dihedral : 5.279 27.291 4184 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.21 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: -1.04 (0.13), residues: 3848 helix: 0.40 (0.10), residues: 2534 sheet: -1.88 (0.31), residues: 236 loop : -3.00 (0.16), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 440 TYR 0.018 0.001 TYR D1089 PHE 0.012 0.001 PHE D 827 TRP 0.025 0.001 TRP A 592 HIS 0.003 0.001 HIS C1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (26748) covalent geometry : angle 0.51070 / 0.28 (36822) hydrogen bonds : bond 0.03437 / 2.46 ( 1929) hydrogen bonds : angle 4.31974 / 3.16 ( 5751) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: C 499 LEU cc_start: 0.9865 (mt) cc_final: 0.9572 (tp) REVERT: C 876 MET cc_start: 0.8677 (mtm) cc_final: 0.8308 (tmm) REVERT: C 1143 MET cc_start: 0.9440 (mmt) cc_final: 0.8840 (ttm) REVERT: C 1155 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8639 (tm-30) REVERT: C 1429 ASP cc_start: 0.4467 (t0) cc_final: 0.3749 (p0) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0377 time to fit residues: 4.3134 Evaluate side-chains 46 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.286 Evaluate side-chains 57 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: D 668 CYS cc_start: 0.9449 (m) cc_final: 0.9121 (p) REVERT: D 700 HIS cc_start: 0.9015 (m90) cc_final: 0.8637 (m-70) REVERT: D 711 GLN cc_start: 0.9589 (mm-40) cc_final: 0.9296 (mm-40) REVERT: D 1140 GLU cc_start: 0.9091 (tt0) cc_final: 0.8536 (tm-30) REVERT: D 1143 MET cc_start: 0.9644 (mmt) cc_final: 0.9180 (mmm) REVERT: D 1169 LYS cc_start: 0.9569 (mttt) cc_final: 0.9303 (tttt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0363 time to fit residues: 3.5189 Evaluate side-chains 46 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 42 optimal weight: 10.0000 chunk 333 optimal weight: 30.0000 chunk 61 optimal weight: 40.0000 chunk 312 optimal weight: 9.9990 chunk 221 optimal weight: 30.0000 chunk 297 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 408 optimal weight: 0.3980 chunk 159 optimal weight: 20.0000 chunk 289 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 overall best weight: 6.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 47 ASN C 144 ASN C 259 HIS C 605 GLN C 656 HIS C 707 HIS C1081 GLN D 47 ASN ** D 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 707 HIS ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1164 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.042495 restraints weight = 53180.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.043519 restraints weight = 31329.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.044208 restraints weight = 22011.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.044656 restraints weight = 17209.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.044989 restraints weight = 14537.762| |-----------------------------------------------------------------------------| r_work (final): 0.2792 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.054720 restraints weight = 57097.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055911 restraints weight = 35906.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.056668 restraints weight = 25753.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.057089 restraints weight = 20119.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057318 restraints weight = 17232.142| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2792 r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26748 Z= 0.168 Angle : 0.539 7.621 36822 Z= 0.294 Chirality : 0.037 0.158 4520 Planarity : 0.004 0.049 4802 Dihedral : 4.738 26.650 4184 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.13 % Allowed : 2.70 % Favored : 97.17 % 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: 0.39 (0.14), residues: 3848 helix: 1.59 (0.10), residues: 2536 sheet: -1.79 (0.32), residues: 234 loop : -2.59 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1082 TYR 0.016 0.002 TYR C1259 PHE 0.016 0.002 PHE A 821 TRP 0.023 0.001 TRP A 592 HIS 0.007 0.001 HIS A 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (26748) covalent geometry : angle 0.53940 / 0.29 (36822) hydrogen bonds : bond 0.03171 / 2.27 ( 1929) hydrogen bonds : angle 4.03094 / 2.94 ( 5751) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 499 LEU cc_start: 0.9860 (mt) cc_final: 0.9592 (tp) REVERT: A 650 MET cc_start: 0.9379 (mpp) cc_final: 0.9153 (mpp) REVERT: A 876 MET cc_start: 0.8680 (mtm) cc_final: 0.8332 (tmm) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0422 time to fit residues: 3.5878 Evaluate side-chains 45 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.299 Evaluate side-chains 48 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.251 Fit side-chains REVERT: B 660 GLN cc_start: 0.9298 (mm-40) cc_final: 0.8906 (mm-40) REVERT: B 668 CYS cc_start: 0.9423 (m) cc_final: 0.9079 (p) REVERT: B 700 HIS cc_start: 0.8962 (m90) cc_final: 0.8601 (m-70) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0393 time to fit residues: 3.2655 Evaluate side-chains 44 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 271 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 284 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 339 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 352 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 144 ASN A 605 GLN A 656 HIS A 707 HIS A 711 GLN A1081 GLN B 660 GLN B 707 HIS ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.066868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.045034 restraints weight = 57537.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.045991 restraints weight = 34632.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.046634 restraints weight = 24460.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.046966 restraints weight = 19190.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.047300 restraints weight = 16506.047| |-----------------------------------------------------------------------------| r_work (final): 0.2822 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.078642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055508 restraints weight = 56484.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056690 restraints weight = 35996.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057419 restraints weight = 26043.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.057919 restraints weight = 20483.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.058189 restraints weight = 17392.617| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2822 r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26748 Z= 0.109 Angle : 0.476 7.179 36822 Z= 0.255 Chirality : 0.037 0.148 4520 Planarity : 0.004 0.047 4802 Dihedral : 4.376 26.647 4184 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.21 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: 1.08 (0.14), residues: 3848 helix: 2.14 (0.10), residues: 2536 sheet: -1.68 (0.31), residues: 254 loop : -2.36 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1310 TYR 0.015 0.001 TYR C1259 PHE 0.010 0.001 PHE C 821 TRP 0.048 0.001 TRP A 592 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (26748) covalent geometry : angle 0.47604 / 0.26 (36822) hydrogen bonds : bond 0.02856 / 2.04 ( 1929) hydrogen bonds : angle 3.68894 / 2.69 ( 5751) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: C 499 LEU cc_start: 0.9875 (mt) cc_final: 0.9498 (tp) REVERT: C 876 MET cc_start: 0.8784 (mtm) cc_final: 0.8410 (tmm) REVERT: C 1143 MET cc_start: 0.9304 (mmp) cc_final: 0.8747 (tpp) REVERT: C 1169 LYS cc_start: 0.9056 (mtmm) cc_final: 0.8825 (tttt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0465 time to fit residues: 4.0366 Evaluate side-chains 43 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.267 Evaluate side-chains 52 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.248 Fit side-chains REVERT: B 660 GLN cc_start: 0.8984 (mm110) cc_final: 0.8729 (mm-40) REVERT: B 700 HIS cc_start: 0.8860 (m90) cc_final: 0.8418 (m-70) REVERT: B 1140 GLU cc_start: 0.8840 (tt0) cc_final: 0.8455 (tm-30) REVERT: B 1143 MET cc_start: 0.9296 (mmm) cc_final: 0.9064 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0417 time to fit residues: 3.7194 Evaluate side-chains 43 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 404 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 153 optimal weight: 0.6980 chunk 255 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 316 optimal weight: 0.5980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 47 ASN C 656 HIS C 707 HIS C 711 GLN C1081 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.043367 restraints weight = 51408.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.044408 restraints weight = 31130.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.045099 restraints weight = 21931.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.045529 restraints weight = 17325.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.045884 restraints weight = 14696.971| |-----------------------------------------------------------------------------| r_work (final): 0.2831 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.079240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.058095 restraints weight = 57543.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.058249 restraints weight = 38183.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.058644 restraints weight = 27456.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059013 restraints weight = 22655.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058910 restraints weight = 21928.151| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2831 r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26748 Z= 0.090 Angle : 0.460 6.951 36822 Z= 0.242 Chirality : 0.036 0.148 4520 Planarity : 0.004 0.046 4802 Dihedral : 4.084 26.559 4184 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.13 % Allowed : 2.19 % Favored : 97.69 % 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: 1.54 (0.14), residues: 3848 helix: 2.50 (0.10), residues: 2534 sheet: -1.47 (0.31), residues: 254 loop : -2.20 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1082 TYR 0.025 0.001 TYR B1083 PHE 0.009 0.001 PHE A 821 TRP 0.043 0.001 TRP D 592 HIS 0.003 0.001 HIS A1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 (26748) covalent geometry : angle 0.46043 / 0.24 (36822) hydrogen bonds : bond 0.02641 / 1.88 ( 1929) hydrogen bonds : angle 3.41543 / 2.48 ( 5751) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: C 499 LEU cc_start: 0.9864 (mt) cc_final: 0.9448 (tp) REVERT: C 597 ASP cc_start: 0.9269 (m-30) cc_final: 0.9048 (m-30) REVERT: C 876 MET cc_start: 0.8752 (mtm) cc_final: 0.8409 (tmm) REVERT: C 1143 MET cc_start: 0.9311 (mmp) cc_final: 0.8743 (tpp) REVERT: C 1429 ASP cc_start: 0.4451 (t0) cc_final: 0.3620 (p0) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.0423 time to fit residues: 4.1249 Evaluate side-chains 45 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.263 Evaluate side-chains 52 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: D 668 CYS cc_start: 0.9491 (m) cc_final: 0.9214 (m) REVERT: D 700 HIS cc_start: 0.8760 (m90) cc_final: 0.8472 (m-70) REVERT: D 1140 GLU cc_start: 0.9121 (tt0) cc_final: 0.8621 (tm-30) REVERT: D 1143 MET cc_start: 0.9490 (mmm) cc_final: 0.8800 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0414 time to fit residues: 3.7103 Evaluate side-chains 46 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 404 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 322 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 325 optimal weight: 4.9990 chunk 375 optimal weight: 40.0000 chunk 168 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 90 optimal weight: 40.0000 chunk 190 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 144 ASN C 259 HIS C 605 GLN D 660 GLN ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.065833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.044315 restraints weight = 57537.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.045227 restraints weight = 34705.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045814 restraints weight = 24584.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.046235 restraints weight = 19437.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.046466 restraints weight = 16677.160| |-----------------------------------------------------------------------------| r_work (final): 0.2805 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.077469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056459 restraints weight = 57644.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.056821 restraints weight = 38382.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.056880 restraints weight = 27701.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057087 restraints weight = 23572.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.057007 restraints weight = 22537.650| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2804 r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26748 Z= 0.156 Angle : 0.509 9.954 36822 Z= 0.274 Chirality : 0.037 0.149 4520 Planarity : 0.004 0.057 4802 Dihedral : 4.199 25.587 4184 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: 1.75 (0.14), residues: 3848 helix: 2.64 (0.10), residues: 2544 sheet: -1.58 (0.32), residues: 254 loop : -2.04 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1310 TYR 0.017 0.001 TYR D1083 PHE 0.017 0.001 PHE B 599 TRP 0.034 0.001 TRP B 592 HIS 0.006 0.001 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (26748) covalent geometry : angle 0.50919 / 0.27 (36822) hydrogen bonds : bond 0.02863 / 2.04 ( 1929) hydrogen bonds : angle 3.60029 / 2.62 ( 5751) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: C 499 LEU cc_start: 0.9860 (mt) cc_final: 0.9543 (tp) REVERT: C 650 MET cc_start: 0.9529 (mpp) cc_final: 0.9267 (mpp) REVERT: C 876 MET cc_start: 0.8666 (mtm) cc_final: 0.8329 (tmm) REVERT: C 1143 MET cc_start: 0.9342 (mmp) cc_final: 0.8759 (tpp) REVERT: C 1429 ASP cc_start: 0.4627 (t0) cc_final: 0.3756 (p0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0464 time to fit residues: 4.1089 Evaluate side-chains 41 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.257 Evaluate side-chains 46 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.162 Fit side-chains REVERT: B 1143 MET cc_start: 0.9578 (mmm) cc_final: 0.9106 (tpp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0331 time to fit residues: 2.7840 Evaluate side-chains 37 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 169 optimal weight: 50.0000 chunk 340 optimal weight: 3.9990 chunk 8 optimal weight: 30.0000 chunk 118 optimal weight: 0.1980 chunk 294 optimal weight: 70.0000 chunk 13 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 210 optimal weight: 20.0000 chunk 398 optimal weight: 6.9990 chunk 241 optimal weight: 0.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.064916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.042760 restraints weight = 52039.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.043765 restraints weight = 31182.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.044446 restraints weight = 21969.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.044917 restraints weight = 17183.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.045221 restraints weight = 14449.042| |-----------------------------------------------------------------------------| r_work (final): 0.2816 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.078117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057373 restraints weight = 58102.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.057706 restraints weight = 40796.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057321 restraints weight = 30775.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057411 restraints weight = 29696.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.057539 restraints weight = 26937.412| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2816 r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26748 Z= 0.114 Angle : 0.485 10.701 36822 Z= 0.256 Chirality : 0.036 0.162 4520 Planarity : 0.004 0.045 4802 Dihedral : 4.056 26.030 4184 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 1.93 (0.14), residues: 3848 helix: 2.76 (0.10), residues: 2544 sheet: -1.52 (0.33), residues: 246 loop : -1.92 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 440 TYR 0.018 0.001 TYR D1083 PHE 0.010 0.001 PHE C 665 TRP 0.040 0.001 TRP D 615 HIS 0.003 0.001 HIS B 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (26748) covalent geometry : angle 0.48450 / 0.26 (36822) hydrogen bonds : bond 0.02766 / 1.96 ( 1929) hydrogen bonds : angle 3.41174 / 2.48 ( 5751) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 876 MET cc_start: 0.8767 (mtm) cc_final: 0.8424 (tmm) REVERT: A 1143 MET cc_start: 0.9316 (mmp) cc_final: 0.8716 (tpp) REVERT: A 1429 ASP cc_start: 0.4335 (t0) cc_final: 0.3493 (p0) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0429 time to fit residues: 3.7855 Evaluate side-chains 41 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.266 Evaluate side-chains 51 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.241 Fit side-chains REVERT: D 1143 MET cc_start: 0.9551 (mmm) cc_final: 0.9123 (tpp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0427 time to fit residues: 3.7241 Evaluate side-chains 40 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 149 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 40.0000 chunk 326 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 94 optimal weight: 30.0000 chunk 376 optimal weight: 7.9990 chunk 373 optimal weight: 0.0060 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 0.0170 chunk 132 optimal weight: 6.9990 overall best weight: 2.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.066704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.045207 restraints weight = 56772.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.046122 restraints weight = 34867.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046749 restraints weight = 24719.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.047139 restraints weight = 19627.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.047350 restraints weight = 16829.901| |-----------------------------------------------------------------------------| r_work (final): 0.2836 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.078742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057605 restraints weight = 57104.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.057859 restraints weight = 38143.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.058003 restraints weight = 28805.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.058343 restraints weight = 23760.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.058260 restraints weight = 21826.116| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2835 r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 26748 Z= 0.096 Angle : 0.465 7.715 36822 Z= 0.243 Chirality : 0.036 0.142 4520 Planarity : 0.003 0.045 4802 Dihedral : 3.882 25.814 4184 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 2.13 (0.14), residues: 3848 helix: 2.90 (0.10), residues: 2556 sheet: -1.38 (0.33), residues: 254 loop : -1.89 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1162 TYR 0.018 0.001 TYR D1083 PHE 0.013 0.001 PHE D 665 TRP 0.031 0.001 TRP B 615 HIS 0.002 0.000 HIS B 656 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (26748) covalent geometry : angle 0.46456 / 0.24 (36822) hydrogen bonds : bond 0.02565 / 1.83 ( 1929) hydrogen bonds : angle 3.27222 / 2.37 ( 5751) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.275 Fit side-chains REVERT: A 438 TRP cc_start: 0.9322 (m-10) cc_final: 0.8683 (m-10) REVERT: A 650 MET cc_start: 0.9516 (mpp) cc_final: 0.9204 (mpp) REVERT: A 876 MET cc_start: 0.8795 (mtm) cc_final: 0.8438 (tmm) REVERT: A 1143 MET cc_start: 0.9312 (mmp) cc_final: 0.8700 (tpp) REVERT: A 1429 ASP cc_start: 0.4496 (t0) cc_final: 0.3674 (p0) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0453 time to fit residues: 4.1372 Evaluate side-chains 42 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.268 Evaluate side-chains 52 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.207 Fit side-chains REVERT: D 1140 GLU cc_start: 0.8938 (pp20) cc_final: 0.8719 (pp20) REVERT: D 1143 MET cc_start: 0.9528 (mmm) cc_final: 0.9100 (tpp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0465 time to fit residues: 3.9696 Evaluate side-chains 46 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 334 optimal weight: 5.9990 chunk 66 optimal weight: 40.0000 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 363 optimal weight: 10.0000 chunk 249 optimal weight: 2.9990 chunk 403 optimal weight: 50.0000 chunk 378 optimal weight: 0.3980 chunk 234 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.065890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.043867 restraints weight = 52035.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.044921 restraints weight = 31121.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.045628 restraints weight = 21755.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.046066 restraints weight = 16999.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046417 restraints weight = 14346.399| |-----------------------------------------------------------------------------| r_work (final): 0.2847 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.079211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058285 restraints weight = 58297.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.058194 restraints weight = 38437.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058434 restraints weight = 33297.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.059096 restraints weight = 25833.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.058861 restraints weight = 22714.920| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2848 r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26748 Z= 0.093 Angle : 0.464 7.571 36822 Z= 0.243 Chirality : 0.036 0.138 4520 Planarity : 0.004 0.114 4802 Dihedral : 3.811 26.106 4184 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 2.21 (0.14), residues: 3848 helix: 2.95 (0.10), residues: 2558 sheet: -1.33 (0.33), residues: 254 loop : -1.83 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1162 TYR 0.014 0.001 TYR A1259 PHE 0.013 0.001 PHE C 665 TRP 0.028 0.001 TRP D 615 HIS 0.012 0.001 HIS C1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (26748) covalent geometry : angle 0.46373 / 0.24 (36822) hydrogen bonds : bond 0.02495 / 1.77 ( 1929) hydrogen bonds : angle 3.18437 / 2.31 ( 5751) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.276 Fit side-chains REVERT: C 438 TRP cc_start: 0.9304 (m-10) cc_final: 0.8707 (m-10) REVERT: C 876 MET cc_start: 0.8769 (mtm) cc_final: 0.8434 (tmm) REVERT: C 1143 MET cc_start: 0.9325 (mmp) cc_final: 0.8716 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0387 time to fit residues: 3.5233 Evaluate side-chains 40 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.251 Evaluate side-chains 52 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.235 Fit side-chains REVERT: D 1140 GLU cc_start: 0.8876 (pp20) cc_final: 0.8652 (pp20) REVERT: D 1143 MET cc_start: 0.9501 (mmm) cc_final: 0.9067 (tpp) REVERT: D 1169 LYS cc_start: 0.8914 (tmtt) cc_final: 0.8711 (tttm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0412 time to fit residues: 3.6495 Evaluate side-chains 43 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 352 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 381 optimal weight: 50.0000 chunk 7 optimal weight: 0.0070 chunk 90 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 317 optimal weight: 30.0000 chunk 402 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 151 optimal weight: 0.0170 chunk 27 optimal weight: 3.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.066337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.044004 restraints weight = 51307.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045080 restraints weight = 31017.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045808 restraints weight = 21820.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.046297 restraints weight = 16985.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.046599 restraints weight = 14268.444| |-----------------------------------------------------------------------------| r_work (final): 0.2860 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.079630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.058104 restraints weight = 57621.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058882 restraints weight = 39124.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058878 restraints weight = 28136.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059097 restraints weight = 24935.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.059173 restraints weight = 21799.477| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2860 r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 26748 Z= 0.084 Angle : 0.450 6.994 36822 Z= 0.233 Chirality : 0.036 0.143 4520 Planarity : 0.004 0.092 4802 Dihedral : 3.622 25.174 4184 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 2.36 (0.15), residues: 3848 helix: 3.04 (0.10), residues: 2568 sheet: -1.23 (0.34), residues: 254 loop : -1.75 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1162 TYR 0.016 0.001 TYR B1083 PHE 0.015 0.001 PHE D 665 TRP 0.025 0.001 TRP B 615 HIS 0.008 0.001 HIS D1161 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.08 (26748) covalent geometry : angle 0.45031 / 0.23 (36822) hydrogen bonds : bond 0.02371 / 1.68 ( 1929) hydrogen bonds : angle 3.04120 / 2.20 ( 5751) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.286 Fit side-chains REVERT: C 438 TRP cc_start: 0.9269 (m-10) cc_final: 0.8718 (m-10) REVERT: C 876 MET cc_start: 0.8765 (mtm) cc_final: 0.8439 (tmm) REVERT: C 1143 MET cc_start: 0.9297 (mmp) cc_final: 0.8713 (tpp) REVERT: C 1169 LYS cc_start: 0.9022 (ptpp) cc_final: 0.8676 (pttt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0469 time to fit residues: 4.4178 Evaluate side-chains 42 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.325 Evaluate side-chains 50 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.291 Fit side-chains REVERT: D 1143 MET cc_start: 0.9516 (mmm) cc_final: 0.9089 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0420 time to fit residues: 3.6661 Evaluate side-chains 46 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 148 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 320 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 chunk 64 optimal weight: 8.9990 chunk 253 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.045862 restraints weight = 57236.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.046787 restraints weight = 34867.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.047388 restraints weight = 24782.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.047819 restraints weight = 19638.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.048040 restraints weight = 16670.993| |-----------------------------------------------------------------------------| r_work (final): 0.2853 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.079119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057987 restraints weight = 56837.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.058576 restraints weight = 39279.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.058619 restraints weight = 28146.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058852 restraints weight = 25058.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.058933 restraints weight = 22076.941| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2852 r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26748 Z= 0.097 Angle : 0.459 6.741 36822 Z= 0.239 Chirality : 0.036 0.138 4520 Planarity : 0.004 0.080 4802 Dihedral : 3.589 25.181 4184 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.48 (0.15), residues: 3848 helix: 3.11 (0.10), residues: 2578 sheet: -1.20 (0.34), residues: 254 loop : -1.70 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1162 TYR 0.014 0.001 TYR A1259 PHE 0.009 0.001 PHE B 599 TRP 0.034 0.001 TRP D 601 HIS 0.009 0.001 HIS B1164 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (26748) covalent geometry : angle 0.45947 / 0.24 (36822) hydrogen bonds : bond 0.02402 / 1.70 ( 1929) hydrogen bonds : angle 3.07660 / 2.22 ( 5751) =============================================================================== Job complete usr+sys time: 3239.81 seconds wall clock time: 56 minutes 33.41 seconds (3393.41 seconds total)