Starting phenix.real_space_refine on Sat Jul 4 10:19:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sq0_40692/07_2026/8sq0_40692.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sq0_40692/07_2026/8sq0_40692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sq0_40692/07_2026/8sq0_40692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sq0_40692/07_2026/8sq0_40692.map" model { file = "/net/cci-nas-00/data/ceres_data/8sq0_40692/07_2026/8sq0_40692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sq0_40692/07_2026/8sq0_40692.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 80 5.16 5 C 12818 2.51 5 N 3430 2.21 5 O 3614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19948 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1402, 9769 Classifications: {'peptide': 1402} Incomplete info: {'truncation_to_alanine': 428} Link IDs: {'PTRANS': 41, 'TRANS': 1360} Chain breaks: 4 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1481 Unresolved non-hydrogen angles: 1899 Unresolved non-hydrogen dihedrals: 1194 Unresolved non-hydrogen chiralities: 165 Planarities with less than four sites: {'HIS:plan': 14, 'ASN:plan1': 25, 'GLU:plan': 30, 'GLN:plan1': 17, 'ASP:plan': 36, 'ARG:plan': 22, 'PHE:plan': 12, 'TRP:plan': 4, 'TYR:plan': 12} Unresolved non-hydrogen planarities: 743 Chain: "B" Number of atoms: 9769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1402, 9769 Classifications: {'peptide': 1402} Incomplete info: {'truncation_to_alanine': 428} Link IDs: {'PTRANS': 41, 'TRANS': 1360} Chain breaks: 4 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1481 Unresolved non-hydrogen angles: 1899 Unresolved non-hydrogen dihedrals: 1194 Unresolved non-hydrogen chiralities: 165 Planarities with less than four sites: {'HIS:plan': 14, 'ASN:plan1': 25, 'GLU:plan': 30, 'GLN:plan1': 17, 'ASP:plan': 36, 'ARG:plan': 22, 'PHE:plan': 12, 'TRP:plan': 4, 'TYR:plan': 12} Unresolved non-hydrogen planarities: 743 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'GP7': 1, 'LPP': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'GP7': 1, 'LPP': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.69, per 1000 atoms: 0.24 Number of scatterers: 19948 At special positions: 0 Unit cell: (132.87, 178.19, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 6 15.00 O 3614 8.00 N 3430 7.00 C 12818 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.2 seconds 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5364 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 14 sheets defined 72.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 36 through 60 removed outlier: 3.773A pdb=" N ARG A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 Processing helix chain 'A' and resid 96 through 99 Processing helix chain 'A' and resid 100 through 128 removed outlier: 3.966A pdb=" N ASP A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 161 Processing helix chain 'A' and resid 165 through 189 Processing helix chain 'A' and resid 210 through 215 removed outlier: 4.089A pdb=" N ALA A 215 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 247 through 250 removed outlier: 3.595A pdb=" N PHE A 250 " --> pdb=" O PRO A 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 251 through 270 removed outlier: 3.751A pdb=" N ASN A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 326 removed outlier: 5.582A pdb=" N SER A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.790A pdb=" N ASP A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 390 removed outlier: 3.602A pdb=" N PHE A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.796A pdb=" N MET A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 424 removed outlier: 3.646A pdb=" N GLN A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.731A pdb=" N CYS A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 493 removed outlier: 4.123A pdb=" N GLY A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'A' and resid 502 through 555 removed outlier: 3.843A pdb=" N LEU A 519 " --> pdb=" O ASN A 515 " (cutoff:3.500A) Proline residue: A 540 - end of helix removed outlier: 3.995A pdb=" N SER A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 604 Proline residue: A 566 - end of helix removed outlier: 4.108A pdb=" N PHE A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Proline residue: A 577 - end of helix Proline residue: A 582 - end of helix Processing helix chain 'A' and resid 608 through 612 removed outlier: 4.180A pdb=" N VAL A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.616A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 713 Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 731 through 737 removed outlier: 3.610A pdb=" N ILE A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 743 Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.560A pdb=" N ILE A 751 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 770 removed outlier: 3.881A pdb=" N ARG A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 795 Processing helix chain 'A' and resid 813 through 820 Processing helix chain 'A' and resid 836 through 844 Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 935 through 946 removed outlier: 3.539A pdb=" N TYR A 939 " --> pdb=" O LYS A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 982 Processing helix chain 'A' and resid 987 through 1016 removed outlier: 3.616A pdb=" N TYR A 991 " --> pdb=" O ASN A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1036 Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.933A pdb=" N PHE A1041 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1062 removed outlier: 3.937A pdb=" N ARG A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP A1056 " --> pdb=" O ARG A1052 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A1060 " --> pdb=" O ASP A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1089 removed outlier: 3.707A pdb=" N ASN A1074 " --> pdb=" O GLN A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1138 Proline residue: A1098 - end of helix removed outlier: 4.134A pdb=" N ARG A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Proline residue: A1127 - end of helix Processing helix chain 'A' and resid 1138 through 1146 Processing helix chain 'A' and resid 1147 through 1201 Proline residue: A1168 - end of helix removed outlier: 4.307A pdb=" N ASN A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1248 removed outlier: 4.789A pdb=" N THR A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A1238 " --> pdb=" O GLU A1234 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER A1239 " --> pdb=" O THR A1235 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A1240 " --> pdb=" O ASN A1236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A1246 " --> pdb=" O ARG A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1320 removed outlier: 3.893A pdb=" N LEU A1317 " --> pdb=" O SER A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1341 removed outlier: 4.273A pdb=" N GLY A1341 " --> pdb=" O ILE A1337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1337 through 1341' Processing helix chain 'A' and resid 1341 through 1349 Processing helix chain 'A' and resid 1363 through 1368 Processing helix chain 'A' and resid 1374 through 1385 Processing helix chain 'A' and resid 1387 through 1392 Processing helix chain 'A' and resid 1397 through 1400 Processing helix chain 'A' and resid 1413 through 1426 removed outlier: 3.761A pdb=" N LEU A1417 " --> pdb=" O GLY A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1456 removed outlier: 3.524A pdb=" N ARG A1453 " --> pdb=" O GLN A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1473 Processing helix chain 'A' and resid 1492 through 1497 Processing helix chain 'A' and resid 1500 through 1508 Processing helix chain 'B' and resid 29 through 36 Processing helix chain 'B' and resid 36 through 60 removed outlier: 3.774A pdb=" N ARG B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 Processing helix chain 'B' and resid 96 through 99 Processing helix chain 'B' and resid 100 through 128 removed outlier: 3.967A pdb=" N ASP B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 161 Processing helix chain 'B' and resid 165 through 189 Processing helix chain 'B' and resid 210 through 215 removed outlier: 4.088A pdb=" N ALA B 215 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 222 Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 247 through 250 removed outlier: 3.594A pdb=" N PHE B 250 " --> pdb=" O PRO B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 251 through 270 removed outlier: 3.751A pdb=" N ASN B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 326 removed outlier: 5.582A pdb=" N SER B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Proline residue: B 305 - end of helix removed outlier: 3.790A pdb=" N ASP B 324 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 390 removed outlier: 3.603A pdb=" N PHE B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 401 through 411 removed outlier: 3.795A pdb=" N MET B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 424 removed outlier: 3.647A pdb=" N GLN B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.730A pdb=" N CYS B 436 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 493 removed outlier: 4.122A pdb=" N GLY B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) Proline residue: B 460 - end of helix Processing helix chain 'B' and resid 493 through 501 Processing helix chain 'B' and resid 502 through 555 removed outlier: 3.843A pdb=" N LEU B 519 " --> pdb=" O ASN B 515 " (cutoff:3.500A) Proline residue: B 540 - end of helix removed outlier: 3.996A pdb=" N SER B 544 " --> pdb=" O PRO B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 604 Proline residue: B 566 - end of helix removed outlier: 4.108A pdb=" N PHE B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) Proline residue: B 577 - end of helix Proline residue: B 582 - end of helix Processing helix chain 'B' and resid 608 through 612 removed outlier: 4.179A pdb=" N VAL B 612 " --> pdb=" O PRO B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 677 removed outlier: 3.617A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 713 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 731 through 737 removed outlier: 3.609A pdb=" N ILE B 737 " --> pdb=" O ILE B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 743 Processing helix chain 'B' and resid 747 through 751 removed outlier: 3.560A pdb=" N ILE B 751 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 770 removed outlier: 3.882A pdb=" N ARG B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 795 Processing helix chain 'B' and resid 813 through 820 Processing helix chain 'B' and resid 836 through 844 Processing helix chain 'B' and resid 846 through 851 Processing helix chain 'B' and resid 935 through 946 removed outlier: 3.538A pdb=" N TYR B 939 " --> pdb=" O LYS B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 982 Processing helix chain 'B' and resid 987 through 1016 removed outlier: 3.617A pdb=" N TYR B 991 " --> pdb=" O ASN B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1036 Processing helix chain 'B' and resid 1037 through 1044 removed outlier: 3.933A pdb=" N PHE B1041 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1062 removed outlier: 3.937A pdb=" N ARG B1052 " --> pdb=" O ARG B1048 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP B1056 " --> pdb=" O ARG B1052 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE B1057 " --> pdb=" O PHE B1053 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B1060 " --> pdb=" O ASP B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1062 through 1089 removed outlier: 3.708A pdb=" N ASN B1074 " --> pdb=" O GLN B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1138 Proline residue: B1098 - end of helix removed outlier: 4.135A pdb=" N ARG B1115 " --> pdb=" O LEU B1111 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER B1126 " --> pdb=" O SER B1122 " (cutoff:3.500A) Proline residue: B1127 - end of helix Processing helix chain 'B' and resid 1138 through 1146 Processing helix chain 'B' and resid 1147 through 1201 Proline residue: B1168 - end of helix removed outlier: 4.307A pdb=" N ASN B1173 " --> pdb=" O SER B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1205 through 1248 removed outlier: 4.788A pdb=" N THR B1220 " --> pdb=" O ALA B1216 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN B1221 " --> pdb=" O LEU B1217 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR B1222 " --> pdb=" O GLN B1218 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B1238 " --> pdb=" O GLU B1234 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER B1239 " --> pdb=" O THR B1235 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B1240 " --> pdb=" O ASN B1236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B1246 " --> pdb=" O ARG B1242 " (cutoff:3.500A) Processing helix chain 'B' and resid 1313 through 1320 removed outlier: 3.893A pdb=" N LEU B1317 " --> pdb=" O SER B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1337 through 1341 removed outlier: 4.273A pdb=" N GLY B1341 " --> pdb=" O ILE B1337 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1337 through 1341' Processing helix chain 'B' and resid 1341 through 1349 Processing helix chain 'B' and resid 1363 through 1368 Processing helix chain 'B' and resid 1374 through 1385 Processing helix chain 'B' and resid 1387 through 1392 Processing helix chain 'B' and resid 1397 through 1400 Processing helix chain 'B' and resid 1413 through 1426 removed outlier: 3.760A pdb=" N LEU B1417 " --> pdb=" O GLY B1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 1441 through 1456 removed outlier: 3.524A pdb=" N ARG B1453 " --> pdb=" O GLN B1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 1468 through 1473 Processing helix chain 'B' and resid 1492 through 1497 Processing helix chain 'B' and resid 1500 through 1508 Processing sheet with id=AA1, first strand: chain 'A' and resid 645 through 649 removed outlier: 5.268A pdb=" N ALA A 632 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 635 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ARG A 682 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 694 through 696 removed outlier: 6.739A pdb=" N LEU A 658 " --> pdb=" O SER A 822 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ALA A 824 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS A 660 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU A 826 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 662 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 823 " --> pdb=" O GLN A 834 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN A 834 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 825 " --> pdb=" O THR A 832 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 705 through 706 removed outlier: 4.001A pdb=" N GLY A 705 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1287 through 1292 removed outlier: 6.173A pdb=" N THR A1279 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A1290 " --> pdb=" O TYR A1277 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A1277 " --> pdb=" O LYS A1290 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A1292 " --> pdb=" O ASN A1275 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A1275 " --> pdb=" O ILE A1292 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A1272 " --> pdb=" O ILE A1296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1287 through 1292 removed outlier: 6.173A pdb=" N THR A1279 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A1290 " --> pdb=" O TYR A1277 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A1277 " --> pdb=" O LYS A1290 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A1292 " --> pdb=" O ASN A1275 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A1275 " --> pdb=" O ILE A1292 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE A1274 " --> pdb=" O VAL A1331 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A1331 " --> pdb=" O PHE A1274 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN A1276 " --> pdb=" O ASN A1329 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN A1329 " --> pdb=" O ASN A1276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1430 through 1433 removed outlier: 6.886A pdb=" N LEU A1431 " --> pdb=" O LEU A1462 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ILE A1464 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A1433 " --> pdb=" O ILE A1464 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A1302 " --> pdb=" O THR A1463 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS A1301 " --> pdb=" O ARG A1476 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ILE A1478 " --> pdb=" O LYS A1301 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLY A1303 " --> pdb=" O ILE A1478 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU A1480 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL A1305 " --> pdb=" O LEU A1480 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1361 through 1362 Processing sheet with id=AA8, first strand: chain 'B' and resid 645 through 649 removed outlier: 5.267A pdb=" N ALA B 632 " --> pdb=" O ASN B 648 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 635 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ARG B 682 " --> pdb=" O LEU B 635 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 694 through 696 removed outlier: 6.739A pdb=" N LEU B 658 " --> pdb=" O SER B 822 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ALA B 824 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS B 660 " --> pdb=" O ALA B 824 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU B 826 " --> pdb=" O CYS B 660 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 662 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 823 " --> pdb=" O GLN B 834 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN B 834 " --> pdb=" O ILE B 823 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 825 " --> pdb=" O THR B 832 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 705 through 706 removed outlier: 4.001A pdb=" N GLY B 705 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1287 through 1292 removed outlier: 6.174A pdb=" N THR B1279 " --> pdb=" O VAL B1288 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS B1290 " --> pdb=" O TYR B1277 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR B1277 " --> pdb=" O LYS B1290 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE B1292 " --> pdb=" O ASN B1275 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B1275 " --> pdb=" O ILE B1292 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE B1272 " --> pdb=" O ILE B1296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1287 through 1292 removed outlier: 6.174A pdb=" N THR B1279 " --> pdb=" O VAL B1288 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS B1290 " --> pdb=" O TYR B1277 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR B1277 " --> pdb=" O LYS B1290 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE B1292 " --> pdb=" O ASN B1275 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B1275 " --> pdb=" O ILE B1292 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE B1274 " --> pdb=" O VAL B1331 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B1331 " --> pdb=" O PHE B1274 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN B1276 " --> pdb=" O ASN B1329 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN B1329 " --> pdb=" O ASN B1276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1430 through 1433 removed outlier: 6.886A pdb=" N LEU B1431 " --> pdb=" O LEU B1462 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ILE B1464 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B1433 " --> pdb=" O ILE B1464 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B1302 " --> pdb=" O THR B1463 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS B1301 " --> pdb=" O ARG B1476 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE B1478 " --> pdb=" O LYS B1301 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY B1303 " --> pdb=" O ILE B1478 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU B1480 " --> pdb=" O GLY B1303 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B1305 " --> pdb=" O LEU B1480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1361 through 1362 1488 hydrogen bonds defined for protein. 4386 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: 4.57 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 3244 1.29 - 1.42: 5176 1.42 - 1.55: 11717 1.55 - 1.68: 15 1.68 - 1.81: 130 Bond restraints: 20282 Sorted by residual: bond pdb=" O5 LPP A1603 " pdb=" P1 LPP A1603 " ideal model delta sigma weight residual 2.278 1.675 0.603 2.00e-02 2.50e+03 9.10e+02 bond pdb=" O5 LPP B1603 " pdb=" P1 LPP B1603 " ideal model delta sigma weight residual 2.278 1.675 0.603 2.00e-02 2.50e+03 9.09e+02 bond pdb=" O4 LPP B1603 " pdb=" P1 LPP B1603 " ideal model delta sigma weight residual 1.764 1.504 0.260 2.00e-02 2.50e+03 1.70e+02 bond pdb=" O4 LPP A1603 " pdb=" P1 LPP A1603 " ideal model delta sigma weight residual 1.764 1.504 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C6 LPP B1603 " pdb=" O5 LPP B1603 " ideal model delta sigma weight residual 1.243 1.422 -0.179 2.00e-02 2.50e+03 7.99e+01 ... (remaining 20277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.43: 27566 9.43 - 18.86: 26 18.86 - 28.29: 2 28.29 - 37.73: 4 37.73 - 47.16: 2 Bond angle restraints: 27600 Sorted by residual: angle pdb=" O4 LPP A1603 " pdb=" P1 LPP A1603 " pdb=" O5 LPP A1603 " ideal model delta sigma weight residual 62.99 110.15 -47.16 3.00e+00 1.11e-01 2.47e+02 angle pdb=" O4 LPP B1603 " pdb=" P1 LPP B1603 " pdb=" O5 LPP B1603 " ideal model delta sigma weight residual 62.99 110.07 -47.08 3.00e+00 1.11e-01 2.46e+02 angle pdb=" C6 LPP A1603 " pdb=" O5 LPP A1603 " pdb=" P1 LPP A1603 " ideal model delta sigma weight residual 82.33 118.76 -36.43 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C6 LPP B1603 " pdb=" O5 LPP B1603 " pdb=" P1 LPP B1603 " ideal model delta sigma weight residual 82.33 118.75 -36.42 3.00e+00 1.11e-01 1.47e+02 angle pdb=" O2 LPP A1603 " pdb=" P1 LPP A1603 " pdb=" O3 LPP A1603 " ideal model delta sigma weight residual 142.11 109.55 32.56 3.00e+00 1.11e-01 1.18e+02 ... (remaining 27595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.20: 11486 24.20 - 48.40: 448 48.40 - 72.60: 80 72.60 - 96.80: 18 96.80 - 121.00: 2 Dihedral angle restraints: 12034 sinusoidal: 3772 harmonic: 8262 Sorted by residual: dihedral pdb=" CA ARG B 207 " pdb=" C ARG B 207 " pdb=" N LYS B 208 " pdb=" CA LYS B 208 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ARG A 207 " pdb=" C ARG A 207 " pdb=" N LYS A 208 " pdb=" CA LYS A 208 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ARG B 68 " pdb=" C ARG B 68 " pdb=" N ASN B 69 " pdb=" CA ASN B 69 " ideal model delta harmonic sigma weight residual -180.00 -159.40 -20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 12031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1846 0.041 - 0.082: 1019 0.082 - 0.122: 344 0.122 - 0.163: 79 0.163 - 0.204: 14 Chirality restraints: 3302 Sorted by residual: chirality pdb=" CB VAL B 370 " pdb=" CA VAL B 370 " pdb=" CG1 VAL B 370 " pdb=" CG2 VAL B 370 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL A 370 " pdb=" CA VAL A 370 " pdb=" CG1 VAL A 370 " pdb=" CG2 VAL A 370 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA HIS B 364 " pdb=" N HIS B 364 " pdb=" C HIS B 364 " pdb=" CB HIS B 364 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 3299 not shown) Planarity restraints: 3516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1097 " 0.054 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO A1098 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A1098 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1098 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B1097 " -0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO B1098 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B1098 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B1098 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 46 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C ILE B 46 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE B 46 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B 47 " -0.012 2.00e-02 2.50e+03 ... (remaining 3513 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 779 2.70 - 3.25: 21659 3.25 - 3.80: 33308 3.80 - 4.35: 39975 4.35 - 4.90: 69206 Nonbonded interactions: 164927 Sorted by model distance: nonbonded pdb=" OG SER A1022 " pdb=" OD1 ASP A1061 " model vdw 2.146 3.040 nonbonded pdb=" OG SER B1022 " pdb=" OD1 ASP B1061 " model vdw 2.146 3.040 nonbonded pdb=" OH TYR B 386 " pdb=" OG1 THR B1135 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 386 " pdb=" OG1 THR A1135 " model vdw 2.224 3.040 nonbonded pdb=" O VAL A1227 " pdb=" OG1 THR A1230 " model vdw 2.242 3.040 ... (remaining 164922 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 20.520 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.014 0.603 20282 Z= 0.612 Angle : 1.152 47.157 27600 Z= 0.533 Chirality : 0.054 0.204 3302 Planarity : 0.005 0.082 3516 Dihedral : 14.227 121.001 6670 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.26 % 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: -0.38 (0.15), residues: 2784 helix: 0.06 (0.11), residues: 1892 sheet: -0.64 (0.47), residues: 108 loop : -0.62 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1179 TYR 0.031 0.003 TYR A 25 PHE 0.029 0.003 PHE B 302 TRP 0.020 0.003 TRP B 422 HIS 0.014 0.002 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.01379 / 0.61 (20282) covalent geometry : angle 1.15250 / 0.53 (27600) hydrogen bonds : bond 0.08343 / 5.63 ( 1486) hydrogen bonds : angle 5.63941 / 4.17 ( 4386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.697 Fit side-chains REVERT: A 39 ASN cc_start: 0.8449 (t0) cc_final: 0.8108 (t0) REVERT: A 251 SER cc_start: 0.8607 (m) cc_final: 0.8395 (p) REVERT: A 495 LYS cc_start: 0.9234 (mttt) cc_final: 0.8840 (mtpp) REVERT: A 1064 LEU cc_start: 0.8770 (tp) cc_final: 0.8483 (tp) REVERT: A 1100 SER cc_start: 0.8363 (m) cc_final: 0.8072 (m) REVERT: A 1163 MET cc_start: 0.8155 (mmt) cc_final: 0.7232 (mmt) REVERT: A 1244 LYS cc_start: 0.7469 (tppp) cc_final: 0.7049 (mmtt) REVERT: B 39 ASN cc_start: 0.8456 (t0) cc_final: 0.8105 (t0) REVERT: B 251 SER cc_start: 0.8610 (m) cc_final: 0.8400 (p) REVERT: B 495 LYS cc_start: 0.9272 (mttt) cc_final: 0.8917 (mtpp) REVERT: B 1064 LEU cc_start: 0.8775 (tp) cc_final: 0.8480 (tp) REVERT: B 1100 SER cc_start: 0.8359 (m) cc_final: 0.8069 (m) REVERT: B 1163 MET cc_start: 0.8169 (mmt) cc_final: 0.7253 (mmt) REVERT: B 1244 LYS cc_start: 0.7473 (tppp) cc_final: 0.7071 (mmtt) outliers start: 2 outliers final: 0 residues processed: 217 average time/residue: 0.1550 time to fit residues: 51.4273 Evaluate side-chains 175 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS A 365 GLN A 462 ASN A 469 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 HIS B 365 GLN B 462 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117772 restraints weight = 24587.429| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.92 r_work: 0.3253 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20282 Z= 0.163 Angle : 0.541 9.185 27600 Z= 0.293 Chirality : 0.042 0.144 3302 Planarity : 0.004 0.047 3516 Dihedral : 10.181 101.402 3236 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.62 % Allowed : 4.83 % Favored : 94.55 % 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: 0.70 (0.15), residues: 2784 helix: 0.93 (0.12), residues: 1868 sheet: -0.30 (0.50), residues: 110 loop : -0.30 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1052 TYR 0.020 0.002 TYR B1246 PHE 0.021 0.002 PHE B 302 TRP 0.010 0.001 TRP B1014 HIS 0.005 0.001 HIS A1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (20282) covalent geometry : angle 0.54100 / 0.29 (27600) hydrogen bonds : bond 0.04638 / 3.08 ( 1486) hydrogen bonds : angle 4.78521 / 3.56 ( 4386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.451 Fit side-chains REVERT: A 14 ARG cc_start: 0.7262 (mmp80) cc_final: 0.7002 (mmp80) REVERT: A 39 ASN cc_start: 0.8721 (t0) cc_final: 0.8475 (t0) REVERT: A 76 MET cc_start: 0.8710 (mmm) cc_final: 0.8369 (mmt) REVERT: A 251 SER cc_start: 0.8692 (m) cc_final: 0.8348 (p) REVERT: A 495 LYS cc_start: 0.9264 (mttt) cc_final: 0.8848 (mtpp) REVERT: B 14 ARG cc_start: 0.7271 (mmp80) cc_final: 0.7010 (mmp80) REVERT: B 39 ASN cc_start: 0.8732 (t0) cc_final: 0.8485 (t0) REVERT: B 76 MET cc_start: 0.8715 (mmm) cc_final: 0.8395 (mmt) REVERT: B 251 SER cc_start: 0.8701 (m) cc_final: 0.8360 (p) REVERT: B 495 LYS cc_start: 0.9277 (mttt) cc_final: 0.8876 (mtpp) outliers start: 10 outliers final: 6 residues processed: 198 average time/residue: 0.1351 time to fit residues: 41.6744 Evaluate side-chains 171 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 586 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 0 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 123 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.168334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115277 restraints weight = 24789.179| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.93 r_work: 0.3213 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20282 Z= 0.208 Angle : 0.547 8.849 27600 Z= 0.292 Chirality : 0.043 0.162 3302 Planarity : 0.004 0.047 3516 Dihedral : 9.570 88.603 3236 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.30 % Allowed : 7.92 % Favored : 90.78 % 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: 1.05 (0.15), residues: 2784 helix: 1.15 (0.12), residues: 1874 sheet: -0.20 (0.50), residues: 110 loop : -0.04 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 485 TYR 0.027 0.002 TYR A 479 PHE 0.022 0.002 PHE B 302 TRP 0.010 0.001 TRP B1175 HIS 0.008 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (20282) covalent geometry : angle 0.54700 / 0.29 (27600) hydrogen bonds : bond 0.04569 / 3.03 ( 1486) hydrogen bonds : angle 4.66429 / 3.47 ( 4386) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.455 Fit side-chains REVERT: A 14 ARG cc_start: 0.7418 (mmp80) cc_final: 0.7115 (mmp80) REVERT: A 39 ASN cc_start: 0.8766 (t0) cc_final: 0.8547 (t0) REVERT: A 76 MET cc_start: 0.8764 (mmm) cc_final: 0.8413 (mmt) REVERT: A 251 SER cc_start: 0.8542 (m) cc_final: 0.8302 (p) REVERT: A 495 LYS cc_start: 0.9270 (mttt) cc_final: 0.8860 (mtpp) REVERT: A 556 ASP cc_start: 0.8059 (t0) cc_final: 0.7800 (t0) REVERT: B 39 ASN cc_start: 0.8767 (t0) cc_final: 0.8549 (t0) REVERT: B 76 MET cc_start: 0.8761 (mmm) cc_final: 0.8432 (mmt) REVERT: B 251 SER cc_start: 0.8553 (m) cc_final: 0.8316 (p) REVERT: B 495 LYS cc_start: 0.9286 (mttt) cc_final: 0.8907 (mtpp) REVERT: B 556 ASP cc_start: 0.8138 (t0) cc_final: 0.7881 (t0) outliers start: 21 outliers final: 19 residues processed: 203 average time/residue: 0.1385 time to fit residues: 43.8723 Evaluate side-chains 198 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 183 optimal weight: 1.9990 chunk 61 optimal weight: 0.0070 chunk 208 optimal weight: 20.0000 chunk 148 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 266 optimal weight: 30.0000 chunk 89 optimal weight: 1.9990 chunk 276 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS A 462 ASN B 121 HIS B 462 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.168950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116067 restraints weight = 24609.799| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.93 r_work: 0.3230 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20282 Z= 0.185 Angle : 0.517 8.674 27600 Z= 0.276 Chirality : 0.042 0.153 3302 Planarity : 0.004 0.045 3516 Dihedral : 9.102 86.025 3236 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.10 % Allowed : 8.29 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.15), residues: 2784 helix: 1.35 (0.12), residues: 1886 sheet: -0.07 (0.51), residues: 110 loop : 0.11 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1052 TYR 0.026 0.002 TYR B 479 PHE 0.020 0.001 PHE A 302 TRP 0.012 0.001 TRP B1175 HIS 0.006 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (20282) covalent geometry : angle 0.51651 / 0.28 (27600) hydrogen bonds : bond 0.04341 / 2.89 ( 1486) hydrogen bonds : angle 4.55211 / 3.39 ( 4386) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.703 Fit side-chains REVERT: A 39 ASN cc_start: 0.8771 (t0) cc_final: 0.8571 (t0) REVERT: A 76 MET cc_start: 0.8749 (mmm) cc_final: 0.8444 (mmt) REVERT: A 251 SER cc_start: 0.8526 (m) cc_final: 0.8277 (p) REVERT: A 269 GLN cc_start: 0.7245 (tt0) cc_final: 0.6755 (mm110) REVERT: A 478 LYS cc_start: 0.7674 (pttt) cc_final: 0.7465 (ptmm) REVERT: A 489 GLU cc_start: 0.7323 (tm-30) cc_final: 0.7037 (tt0) REVERT: A 495 LYS cc_start: 0.9265 (mttt) cc_final: 0.8851 (mtpp) REVERT: A 556 ASP cc_start: 0.8221 (t0) cc_final: 0.7974 (t0) REVERT: A 941 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 1163 MET cc_start: 0.8630 (mmt) cc_final: 0.8097 (mmt) REVERT: B 14 ARG cc_start: 0.7296 (mmp80) cc_final: 0.7023 (mmp80) REVERT: B 76 MET cc_start: 0.8757 (mmm) cc_final: 0.8427 (mmt) REVERT: B 251 SER cc_start: 0.8534 (m) cc_final: 0.8287 (p) REVERT: B 269 GLN cc_start: 0.7229 (tt0) cc_final: 0.6737 (mm110) REVERT: B 478 LYS cc_start: 0.7716 (pttt) cc_final: 0.7507 (ptmm) REVERT: B 489 GLU cc_start: 0.7305 (tm-30) cc_final: 0.7026 (tt0) REVERT: B 495 LYS cc_start: 0.9286 (mttt) cc_final: 0.8904 (mtpp) REVERT: B 556 ASP cc_start: 0.8255 (t0) cc_final: 0.7964 (t0) REVERT: B 1163 MET cc_start: 0.8632 (mmt) cc_final: 0.8096 (mmt) outliers start: 34 outliers final: 22 residues processed: 233 average time/residue: 0.1466 time to fit residues: 51.8629 Evaluate side-chains 210 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1009 GLN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1176 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 140 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 272 optimal weight: 0.0370 chunk 107 optimal weight: 0.6980 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.168442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115523 restraints weight = 24616.904| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.92 r_work: 0.3221 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20282 Z= 0.200 Angle : 0.521 9.056 27600 Z= 0.279 Chirality : 0.042 0.156 3302 Planarity : 0.004 0.044 3516 Dihedral : 8.894 86.797 3236 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.66 % Allowed : 9.03 % Favored : 88.30 % 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: 1.43 (0.16), residues: 2784 helix: 1.40 (0.12), residues: 1886 sheet: -0.10 (0.50), residues: 110 loop : 0.21 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1052 TYR 0.023 0.002 TYR B 479 PHE 0.021 0.001 PHE B 302 TRP 0.013 0.001 TRP B1175 HIS 0.007 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (20282) covalent geometry : angle 0.52127 / 0.28 (27600) hydrogen bonds : bond 0.04388 / 2.91 ( 1486) hydrogen bonds : angle 4.54498 / 3.38 ( 4386) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.775 Fit side-chains REVERT: A 76 MET cc_start: 0.8771 (mmm) cc_final: 0.8427 (mmt) REVERT: A 251 SER cc_start: 0.8579 (m) cc_final: 0.8341 (p) REVERT: A 269 GLN cc_start: 0.7228 (tt0) cc_final: 0.6755 (mm110) REVERT: A 478 LYS cc_start: 0.7744 (pttt) cc_final: 0.7518 (ptmm) REVERT: A 489 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7119 (tt0) REVERT: A 495 LYS cc_start: 0.9269 (mttt) cc_final: 0.8880 (mtpp) REVERT: A 556 ASP cc_start: 0.8177 (t0) cc_final: 0.7951 (t0) REVERT: A 941 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7825 (mm-30) REVERT: B 76 MET cc_start: 0.8778 (mmm) cc_final: 0.8442 (mmt) REVERT: B 251 SER cc_start: 0.8583 (m) cc_final: 0.8348 (p) REVERT: B 478 LYS cc_start: 0.7707 (pttt) cc_final: 0.7480 (ptmm) REVERT: B 489 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7076 (tt0) REVERT: B 495 LYS cc_start: 0.9281 (mttt) cc_final: 0.8897 (mtpp) REVERT: B 556 ASP cc_start: 0.8207 (t0) cc_final: 0.7964 (t0) outliers start: 43 outliers final: 31 residues processed: 227 average time/residue: 0.1521 time to fit residues: 53.7530 Evaluate side-chains 216 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 1009 GLN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1213 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 158 optimal weight: 0.0070 chunk 26 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 280 optimal weight: 30.0000 chunk 119 optimal weight: 30.0000 chunk 235 optimal weight: 4.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.119319 restraints weight = 24449.992| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.92 r_work: 0.3276 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20282 Z= 0.126 Angle : 0.464 9.415 27600 Z= 0.250 Chirality : 0.040 0.129 3302 Planarity : 0.003 0.043 3516 Dihedral : 8.383 87.582 3236 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.49 % Allowed : 10.95 % Favored : 87.56 % 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 (0.16), residues: 2784 helix: 1.68 (0.12), residues: 1880 sheet: 0.07 (0.51), residues: 110 loop : 0.24 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1052 TYR 0.015 0.001 TYR B 479 PHE 0.016 0.001 PHE A 954 TRP 0.013 0.001 TRP A1175 HIS 0.005 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (20282) covalent geometry : angle 0.46367 / 0.25 (27600) hydrogen bonds : bond 0.04012 / 2.67 ( 1486) hydrogen bonds : angle 4.35832 / 3.26 ( 4386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.789 Fit side-chains REVERT: A 76 MET cc_start: 0.8695 (mmm) cc_final: 0.8433 (mmt) REVERT: A 251 SER cc_start: 0.8533 (m) cc_final: 0.8303 (p) REVERT: A 269 GLN cc_start: 0.7159 (tt0) cc_final: 0.6723 (mm110) REVERT: A 478 LYS cc_start: 0.7763 (pttt) cc_final: 0.7542 (ptmm) REVERT: A 489 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7127 (tt0) REVERT: A 495 LYS cc_start: 0.9269 (mttt) cc_final: 0.8879 (mtpp) REVERT: A 941 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7772 (mm-30) REVERT: A 1163 MET cc_start: 0.8575 (mmt) cc_final: 0.8116 (mmt) REVERT: A 1208 MET cc_start: 0.8624 (mtt) cc_final: 0.8390 (mtt) REVERT: B 76 MET cc_start: 0.8701 (mmm) cc_final: 0.8448 (mmt) REVERT: B 251 SER cc_start: 0.8536 (m) cc_final: 0.8304 (p) REVERT: B 269 GLN cc_start: 0.7155 (tt0) cc_final: 0.6719 (mm110) REVERT: B 478 LYS cc_start: 0.7761 (pttt) cc_final: 0.7547 (ptmm) REVERT: B 489 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7098 (tt0) REVERT: B 495 LYS cc_start: 0.9280 (mttt) cc_final: 0.8899 (mtpp) REVERT: B 1163 MET cc_start: 0.8578 (mmt) cc_final: 0.8115 (mmt) REVERT: B 1208 MET cc_start: 0.8626 (mtt) cc_final: 0.8399 (mtt) outliers start: 24 outliers final: 15 residues processed: 234 average time/residue: 0.1564 time to fit residues: 56.4464 Evaluate side-chains 210 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1009 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 213 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 200 optimal weight: 50.0000 chunk 220 optimal weight: 10.0000 chunk 103 optimal weight: 0.5980 chunk 203 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.167309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114265 restraints weight = 24752.367| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.92 r_work: 0.3201 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20282 Z= 0.225 Angle : 0.538 9.098 27600 Z= 0.286 Chirality : 0.043 0.168 3302 Planarity : 0.004 0.044 3516 Dihedral : 8.622 88.611 3236 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.17 % Allowed : 11.39 % Favored : 86.45 % 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: 1.56 (0.16), residues: 2784 helix: 1.51 (0.12), residues: 1884 sheet: -0.06 (0.51), residues: 110 loop : 0.22 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1052 TYR 0.014 0.002 TYR B 159 PHE 0.023 0.002 PHE B 302 TRP 0.012 0.001 TRP A1175 HIS 0.007 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (20282) covalent geometry : angle 0.53784 / 0.29 (27600) hydrogen bonds : bond 0.04411 / 2.93 ( 1486) hydrogen bonds : angle 4.50036 / 3.35 ( 4386) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.779 Fit side-chains REVERT: A 76 MET cc_start: 0.8790 (mmm) cc_final: 0.8451 (mmt) REVERT: A 159 TYR cc_start: 0.9134 (m-80) cc_final: 0.8834 (m-80) REVERT: A 251 SER cc_start: 0.8574 (m) cc_final: 0.8330 (p) REVERT: A 269 GLN cc_start: 0.7173 (tt0) cc_final: 0.6739 (mm110) REVERT: A 478 LYS cc_start: 0.7788 (pttt) cc_final: 0.7530 (ptmm) REVERT: A 485 ARG cc_start: 0.7319 (ptm-80) cc_final: 0.7051 (tmm-80) REVERT: A 489 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7187 (tt0) REVERT: A 495 LYS cc_start: 0.9268 (mttt) cc_final: 0.8860 (mtpp) REVERT: A 941 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 76 MET cc_start: 0.8793 (mmm) cc_final: 0.8461 (mmt) REVERT: B 159 TYR cc_start: 0.9134 (m-80) cc_final: 0.8834 (m-80) REVERT: B 195 MET cc_start: 0.5218 (ptp) cc_final: 0.4897 (ptp) REVERT: B 251 SER cc_start: 0.8576 (m) cc_final: 0.8333 (p) REVERT: B 269 GLN cc_start: 0.7169 (tt0) cc_final: 0.6737 (mm110) REVERT: B 478 LYS cc_start: 0.7780 (pttt) cc_final: 0.7527 (ptmm) REVERT: B 489 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7177 (tt0) REVERT: B 495 LYS cc_start: 0.9281 (mttt) cc_final: 0.8890 (mtpp) outliers start: 35 outliers final: 28 residues processed: 222 average time/residue: 0.1526 time to fit residues: 52.5618 Evaluate side-chains 217 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1018 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1009 GLN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1123 ILE Chi-restraints excluded: chain B residue 1176 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 50.0000 chunk 214 optimal weight: 7.9990 chunk 197 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 264 optimal weight: 20.0000 chunk 270 optimal weight: 20.0000 chunk 94 optimal weight: 0.0870 chunk 259 optimal weight: 20.0000 chunk 19 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.170034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117401 restraints weight = 24736.786| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.93 r_work: 0.3260 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20282 Z= 0.126 Angle : 0.471 9.472 27600 Z= 0.253 Chirality : 0.040 0.129 3302 Planarity : 0.003 0.043 3516 Dihedral : 8.219 87.899 3236 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.86 % Allowed : 12.19 % Favored : 85.95 % 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: 1.83 (0.16), residues: 2784 helix: 1.73 (0.12), residues: 1880 sheet: 0.07 (0.51), residues: 110 loop : 0.27 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1052 TYR 0.011 0.001 TYR A 506 PHE 0.017 0.001 PHE A 954 TRP 0.014 0.001 TRP B1175 HIS 0.006 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (20282) covalent geometry : angle 0.47112 / 0.25 (27600) hydrogen bonds : bond 0.04016 / 2.67 ( 1486) hydrogen bonds : angle 4.33209 / 3.24 ( 4386) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.785 Fit side-chains REVERT: A 76 MET cc_start: 0.8707 (mmm) cc_final: 0.8425 (mmt) REVERT: A 251 SER cc_start: 0.8542 (m) cc_final: 0.8301 (p) REVERT: A 269 GLN cc_start: 0.7154 (tt0) cc_final: 0.6744 (mm110) REVERT: A 478 LYS cc_start: 0.7797 (pttt) cc_final: 0.7549 (ptmm) REVERT: A 485 ARG cc_start: 0.7320 (ptm-80) cc_final: 0.7037 (tmm-80) REVERT: A 489 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7183 (tt0) REVERT: A 495 LYS cc_start: 0.9266 (mttt) cc_final: 0.8873 (mtpp) REVERT: A 941 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 1163 MET cc_start: 0.8617 (mmt) cc_final: 0.8190 (mmt) REVERT: A 1208 MET cc_start: 0.8562 (mtt) cc_final: 0.8323 (mtt) REVERT: B 76 MET cc_start: 0.8714 (mmm) cc_final: 0.8442 (mmt) REVERT: B 251 SER cc_start: 0.8541 (m) cc_final: 0.8294 (p) REVERT: B 269 GLN cc_start: 0.7140 (tt0) cc_final: 0.6735 (mm110) REVERT: B 478 LYS cc_start: 0.7784 (pttt) cc_final: 0.7541 (ptmm) REVERT: B 485 ARG cc_start: 0.7657 (tmm-80) cc_final: 0.7247 (ptm-80) REVERT: B 489 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7107 (tt0) REVERT: B 495 LYS cc_start: 0.9278 (mttt) cc_final: 0.8899 (mtpp) REVERT: B 1163 MET cc_start: 0.8619 (mmt) cc_final: 0.8187 (mmt) outliers start: 30 outliers final: 22 residues processed: 227 average time/residue: 0.1447 time to fit residues: 51.3108 Evaluate side-chains 212 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1053 PHE Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1009 GLN Chi-restraints excluded: chain B residue 1053 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1220 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 242 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 81 optimal weight: 30.0000 chunk 234 optimal weight: 20.0000 chunk 153 optimal weight: 0.5980 chunk 188 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 271 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.166700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113558 restraints weight = 24798.531| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.94 r_work: 0.3206 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20282 Z= 0.213 Angle : 0.539 9.212 27600 Z= 0.284 Chirality : 0.042 0.159 3302 Planarity : 0.004 0.044 3516 Dihedral : 8.429 88.360 3236 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.04 % Allowed : 12.07 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.16), residues: 2784 helix: 1.59 (0.12), residues: 1884 sheet: -0.14 (0.51), residues: 110 loop : 0.25 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1052 TYR 0.014 0.002 TYR B 159 PHE 0.023 0.002 PHE B 302 TRP 0.013 0.001 TRP B1175 HIS 0.007 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (20282) covalent geometry : angle 0.53857 / 0.28 (27600) hydrogen bonds : bond 0.04353 / 2.89 ( 1486) hydrogen bonds : angle 4.46583 / 3.32 ( 4386) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.796 Fit side-chains REVERT: A 76 MET cc_start: 0.8782 (mmm) cc_final: 0.8435 (mmt) REVERT: A 159 TYR cc_start: 0.9122 (m-80) cc_final: 0.8796 (m-80) REVERT: A 195 MET cc_start: 0.5266 (ptp) cc_final: 0.4969 (ptp) REVERT: A 251 SER cc_start: 0.8565 (m) cc_final: 0.8320 (p) REVERT: A 269 GLN cc_start: 0.7158 (tt0) cc_final: 0.6755 (mm110) REVERT: A 478 LYS cc_start: 0.7811 (pttt) cc_final: 0.7542 (ptmm) REVERT: A 485 ARG cc_start: 0.7277 (ptm-80) cc_final: 0.7010 (tmm-80) REVERT: A 489 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7215 (tt0) REVERT: A 495 LYS cc_start: 0.9270 (mttt) cc_final: 0.8860 (mtpp) REVERT: A 941 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7660 (mm-30) REVERT: B 76 MET cc_start: 0.8793 (mmm) cc_final: 0.8455 (mmt) REVERT: B 159 TYR cc_start: 0.9122 (m-80) cc_final: 0.8796 (m-80) REVERT: B 195 MET cc_start: 0.5329 (ptp) cc_final: 0.5033 (ptp) REVERT: B 251 SER cc_start: 0.8562 (m) cc_final: 0.8321 (p) REVERT: B 269 GLN cc_start: 0.7154 (tt0) cc_final: 0.6752 (mm110) REVERT: B 478 LYS cc_start: 0.7806 (pttt) cc_final: 0.7546 (ptmm) REVERT: B 489 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7233 (tt0) REVERT: B 495 LYS cc_start: 0.9278 (mttt) cc_final: 0.8894 (mtpp) outliers start: 33 outliers final: 28 residues processed: 216 average time/residue: 0.1500 time to fit residues: 50.1576 Evaluate side-chains 215 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1009 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1220 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 90 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 195 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 237 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 266 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 259 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118273 restraints weight = 24548.821| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.91 r_work: 0.3257 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20282 Z= 0.133 Angle : 0.485 9.463 27600 Z= 0.259 Chirality : 0.040 0.131 3302 Planarity : 0.003 0.043 3516 Dihedral : 8.030 87.328 3236 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.55 % Allowed : 13.06 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.16), residues: 2784 helix: 1.77 (0.12), residues: 1882 sheet: -0.10 (0.51), residues: 110 loop : 0.31 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1052 TYR 0.010 0.001 TYR A1105 PHE 0.017 0.001 PHE A 576 TRP 0.014 0.001 TRP B1175 HIS 0.007 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (20282) covalent geometry : angle 0.48535 / 0.26 (27600) hydrogen bonds : bond 0.04039 / 2.69 ( 1486) hydrogen bonds : angle 4.33881 / 3.24 ( 4386) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.733 Fit side-chains REVERT: A 76 MET cc_start: 0.8713 (mmm) cc_final: 0.8434 (mmt) REVERT: A 195 MET cc_start: 0.5253 (ptp) cc_final: 0.4765 (ptp) REVERT: A 251 SER cc_start: 0.8532 (m) cc_final: 0.8297 (p) REVERT: A 269 GLN cc_start: 0.7146 (tt0) cc_final: 0.6759 (mm110) REVERT: A 478 LYS cc_start: 0.7812 (pttt) cc_final: 0.7555 (ptmm) REVERT: A 485 ARG cc_start: 0.7216 (ptm-80) cc_final: 0.7003 (tmm-80) REVERT: A 489 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7170 (tt0) REVERT: A 495 LYS cc_start: 0.9266 (mttt) cc_final: 0.8853 (mtpp) REVERT: A 941 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7622 (mm-30) REVERT: A 1163 MET cc_start: 0.8636 (mmt) cc_final: 0.8179 (mmt) REVERT: A 1208 MET cc_start: 0.8539 (mtt) cc_final: 0.8293 (mtt) REVERT: B 43 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8506 (mt) REVERT: B 76 MET cc_start: 0.8719 (mmm) cc_final: 0.8462 (mmt) REVERT: B 195 MET cc_start: 0.5251 (ptp) cc_final: 0.4760 (ptp) REVERT: B 251 SER cc_start: 0.8533 (m) cc_final: 0.8295 (p) REVERT: B 269 GLN cc_start: 0.7138 (tt0) cc_final: 0.6751 (mm110) REVERT: B 478 LYS cc_start: 0.7805 (pttt) cc_final: 0.7550 (ptmm) REVERT: B 485 ARG cc_start: 0.7657 (tmm-80) cc_final: 0.7288 (ptm-80) REVERT: B 495 LYS cc_start: 0.9274 (mttt) cc_final: 0.8881 (mtpp) REVERT: B 1163 MET cc_start: 0.8640 (mmt) cc_final: 0.8180 (mmt) REVERT: B 1245 GLU cc_start: 0.8261 (tt0) cc_final: 0.7853 (tt0) outliers start: 25 outliers final: 22 residues processed: 213 average time/residue: 0.1613 time to fit residues: 52.2857 Evaluate side-chains 205 residues out of total 2472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1053 PHE Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 1009 GLN Chi-restraints excluded: chain B residue 1053 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1100 SER Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1220 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 157 optimal weight: 2.9990 chunk 280 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 279 optimal weight: 8.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.168151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114810 restraints weight = 24716.674| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.93 r_work: 0.3235 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20282 Z= 0.166 Angle : 0.506 9.362 27600 Z= 0.269 Chirality : 0.041 0.142 3302 Planarity : 0.003 0.044 3516 Dihedral : 8.025 87.508 3236 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.92 % Allowed : 12.69 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.16), residues: 2784 helix: 1.72 (0.12), residues: 1888 sheet: -0.19 (0.51), residues: 110 loop : 0.29 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1052 TYR 0.011 0.001 TYR B 159 PHE 0.019 0.001 PHE B 576 TRP 0.013 0.001 TRP B1175 HIS 0.007 0.001 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (20282) covalent geometry : angle 0.50634 / 0.27 (27600) hydrogen bonds : bond 0.04145 / 2.76 ( 1486) hydrogen bonds : angle 4.37793 / 3.27 ( 4386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6104.44 seconds wall clock time: 104 minutes 52.18 seconds (6292.18 seconds total)