Starting phenix.real_space_refine on Thu Sep 26 20:39:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/09_2024/8p50_17435.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/09_2024/8p50_17435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/09_2024/8p50_17435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/09_2024/8p50_17435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/09_2024/8p50_17435.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/09_2024/8p50_17435.cif" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 8611 2.51 5 N 2426 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13714 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1574, 12389 Classifications: {'peptide': 1574} Link IDs: {'PTRANS': 59, 'TRANS': 1514} Chain breaks: 1 Chain: "B" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1292 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 3, 'TRANS': 157} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 865 residue: pdb=" N SER A 5 " occ=0.82 ... (4 atoms not shown) pdb=" OG SER A 5 " occ=0.00 residue: pdb=" N ASP A 7 " occ=0.16 ... (6 atoms not shown) pdb=" OD2 ASP A 7 " occ=0.00 residue: pdb=" N PHE A 8 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 8 " occ=0.00 residue: pdb=" N THR A 9 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 9 " occ=0.00 residue: pdb=" N LEU A 11 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 11 " occ=0.61 residue: pdb=" N ASN A 13 " occ=0.05 ... (6 atoms not shown) pdb=" ND2 ASN A 13 " occ=0.19 residue: pdb=" N THR A 14 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 14 " occ=0.00 residue: pdb=" N ILE A 16 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE A 16 " occ=0.90 residue: pdb=" N ASP A 17 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 17 " occ=0.00 residue: pdb=" N GLY A 18 " occ=0.31 ... (2 atoms not shown) pdb=" O GLY A 18 " occ=0.39 residue: pdb=" N GLN A 19 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN A 19 " occ=0.00 residue: pdb=" N ILE A 20 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE A 20 " occ=0.00 ... (remaining 853 not shown) Time building chain proxies: 8.25, per 1000 atoms: 0.60 Number of scatterers: 13714 At special positions: 0 Unit cell: (99.9, 111.6, 150.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 3 15.00 Mg 1 11.99 O 2632 8.00 N 2426 7.00 C 8611 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.7 seconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3242 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 54.6% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.521A pdb=" N ASP A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.526A pdb=" N GLN A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 93 through 132 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 147 through 170 removed outlier: 4.436A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 202 Processing helix chain 'A' and resid 203 through 216 removed outlier: 4.581A pdb=" N ALA A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALA A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.120A pdb=" N ARG A 300 " --> pdb=" O PRO A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 321 Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'A' and resid 465 through 489 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 517 removed outlier: 3.900A pdb=" N ARG A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.629A pdb=" N VAL A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 558 Processing helix chain 'A' and resid 561 through 573 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 577 through 583 removed outlier: 3.925A pdb=" N VAL A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 577 through 583' Processing helix chain 'A' and resid 586 through 589 Processing helix chain 'A' and resid 590 through 598 Processing helix chain 'A' and resid 598 through 623 removed outlier: 4.351A pdb=" N GLU A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 659 through 664 removed outlier: 3.568A pdb=" N ASP A 662 " --> pdb=" O GLU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 675 through 698 removed outlier: 4.074A pdb=" N LEU A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 691 " --> pdb=" O PHE A 687 " (cutoff:3.500A) Proline residue: A 692 - end of helix removed outlier: 3.921A pdb=" N SER A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 735 through 740 removed outlier: 3.542A pdb=" N ARG A 740 " --> pdb=" O GLN A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 Processing helix chain 'A' and resid 763 through 773 Processing helix chain 'A' and resid 781 through 789 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 800 through 818 Processing helix chain 'A' and resid 823 through 834 removed outlier: 5.029A pdb=" N VAL A 829 " --> pdb=" O GLU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 857 removed outlier: 3.714A pdb=" N GLU A 855 " --> pdb=" O LYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 878 removed outlier: 3.812A pdb=" N ARG A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Proline residue: A 875 - end of helix Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 949 through 953 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1052 through 1056 Processing helix chain 'A' and resid 1065 through 1070 removed outlier: 3.922A pdb=" N TYR A1069 " --> pdb=" O ASP A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1152 removed outlier: 3.811A pdb=" N GLN A1133 " --> pdb=" O ARG A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1175 No H-bonds generated for 'chain 'A' and resid 1173 through 1175' Processing helix chain 'A' and resid 1176 through 1209 removed outlier: 4.003A pdb=" N GLN A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A1197 " --> pdb=" O ASP A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1259 removed outlier: 3.621A pdb=" N LYS A1222 " --> pdb=" O ASN A1218 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR A1237 " --> pdb=" O ALA A1233 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL A1238 " --> pdb=" O GLN A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1263 Processing helix chain 'A' and resid 1281 through 1289 Processing helix chain 'A' and resid 1299 through 1308 Processing helix chain 'A' and resid 1321 through 1332 Processing helix chain 'A' and resid 1335 through 1358 Processing helix chain 'A' and resid 1361 through 1374 removed outlier: 4.282A pdb=" N PHE A1365 " --> pdb=" O GLN A1361 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER A1366 " --> pdb=" O THR A1362 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU A1367 " --> pdb=" O ALA A1363 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A1373 " --> pdb=" O PHE A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1429 removed outlier: 3.737A pdb=" N ARG A1402 " --> pdb=" O TYR A1398 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A1406 " --> pdb=" O ARG A1402 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N GLU A1413 " --> pdb=" O ALA A1409 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ALA A1414 " --> pdb=" O SER A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1448 through 1454 removed outlier: 3.715A pdb=" N VAL A1452 " --> pdb=" O ASN A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1473 Processing helix chain 'A' and resid 1515 through 1528 Processing helix chain 'A' and resid 1531 through 1536 Processing helix chain 'A' and resid 1553 through 1558 removed outlier: 3.857A pdb=" N ALA A1558 " --> pdb=" O THR A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1589 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 71 through 82 Proline residue: B 76 - end of helix removed outlier: 4.115A pdb=" N ARG B 79 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 82 " --> pdb=" O ARG B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 165 through 178 Processing sheet with id=AA1, first strand: chain 'A' and resid 335 through 339 removed outlier: 3.584A pdb=" N GLY A 360 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 339 removed outlier: 3.584A pdb=" N GLY A 360 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE A 361 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 273 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 363 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLY A 271 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASN A 274 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 240 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 454 Processing sheet with id=AA6, first strand: chain 'A' and resid 720 through 722 Processing sheet with id=AA7, first strand: chain 'A' and resid 946 through 948 removed outlier: 5.792A pdb=" N THR A 946 " --> pdb=" O TYR A 974 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 976 " --> pdb=" O THR A 946 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER A 948 " --> pdb=" O LEU A 976 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N TYR A 978 " --> pdb=" O SER A 948 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 963 " --> pdb=" O THR A 979 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 962 " --> pdb=" O ALA A 993 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 993 " --> pdb=" O GLY A 962 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A1022 " --> pdb=" O PRO A 992 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR A1025 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A1081 " --> pdb=" O THR A1025 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 946 through 948 removed outlier: 5.792A pdb=" N THR A 946 " --> pdb=" O TYR A 974 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 976 " --> pdb=" O THR A 946 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER A 948 " --> pdb=" O LEU A 976 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N TYR A 978 " --> pdb=" O SER A 948 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 963 " --> pdb=" O THR A 979 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 962 " --> pdb=" O ALA A 993 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 993 " --> pdb=" O GLY A 962 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A1022 " --> pdb=" O PRO A 992 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR A1025 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A1081 " --> pdb=" O THR A1025 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1009 through 1014 removed outlier: 3.834A pdb=" N ALA A1009 " --> pdb=" O HIS A1047 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A1033 " --> pdb=" O VAL A1064 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER A1037 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A1060 " --> pdb=" O SER A1037 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1377 through 1379 removed outlier: 3.509A pdb=" N SER A1477 " --> pdb=" O SER A1492 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AB3, first strand: chain 'B' and resid 51 through 58 removed outlier: 6.739A pdb=" N ILE B 20 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B 68 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET B 22 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG B 19 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE B 89 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 21 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL B 91 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 23 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ASP B 93 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 88 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE B 124 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE B 90 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN B 126 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 92 " --> pdb=" O ASN B 126 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2136 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: 6.46 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4656 1.34 - 1.46: 2462 1.46 - 1.57: 6764 1.57 - 1.69: 5 1.69 - 1.81: 80 Bond restraints: 13967 Sorted by residual: bond pdb=" CD ARG A1530 " pdb=" NE ARG A1530 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.37e+00 bond pdb=" CA ARG A1530 " pdb=" CB ARG A1530 " ideal model delta sigma weight residual 1.529 1.508 0.021 1.40e-02 5.10e+03 2.19e+00 bond pdb=" CA GLY A 678 " pdb=" C GLY A 678 " ideal model delta sigma weight residual 1.517 1.502 0.015 1.08e-02 8.57e+03 1.89e+00 bond pdb=" C THR A 305 " pdb=" N PRO A 306 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.78e+00 bond pdb=" CB GLU A 207 " pdb=" CG GLU A 207 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.65e+00 ... (remaining 13962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 17585 1.59 - 3.18: 1122 3.18 - 4.76: 162 4.76 - 6.35: 36 6.35 - 7.94: 10 Bond angle restraints: 18915 Sorted by residual: angle pdb=" C PRO A 91 " pdb=" N GLY A 92 " pdb=" CA GLY A 92 " ideal model delta sigma weight residual 119.92 123.41 -3.49 9.60e-01 1.09e+00 1.32e+01 angle pdb=" N SER A 301 " pdb=" CA SER A 301 " pdb=" C SER A 301 " ideal model delta sigma weight residual 109.81 117.73 -7.92 2.21e+00 2.05e-01 1.28e+01 angle pdb=" C LYS A1357 " pdb=" N VAL A1358 " pdb=" CA VAL A1358 " ideal model delta sigma weight residual 121.97 115.63 6.34 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C THR B 48 " pdb=" N ILE B 49 " pdb=" CA ILE B 49 " ideal model delta sigma weight residual 120.77 125.71 -4.94 1.46e+00 4.69e-01 1.15e+01 angle pdb=" CA ARG A 344 " pdb=" CB ARG A 344 " pdb=" CG ARG A 344 " ideal model delta sigma weight residual 114.10 107.49 6.61 2.00e+00 2.50e-01 1.09e+01 ... (remaining 18910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.87: 8291 32.87 - 65.74: 122 65.74 - 98.61: 31 98.61 - 131.47: 2 131.47 - 164.34: 3 Dihedral angle restraints: 8449 sinusoidal: 3411 harmonic: 5038 Sorted by residual: dihedral pdb=" O3B GTP B1001 " pdb=" O3A GTP B1001 " pdb=" PB GTP B1001 " pdb=" PA GTP B1001 " ideal model delta sinusoidal sigma weight residual -68.92 95.42 -164.34 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C8 GTP B1001 " pdb=" C1' GTP B1001 " pdb=" N9 GTP B1001 " pdb=" O4' GTP B1001 " ideal model delta sinusoidal sigma weight residual 104.59 -55.97 160.57 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' GTP B1001 " pdb=" O5' GTP B1001 " pdb=" PA GTP B1001 " pdb=" O3A GTP B1001 " ideal model delta sinusoidal sigma weight residual 69.27 -63.95 133.22 1 2.00e+01 2.50e-03 4.04e+01 ... (remaining 8446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1360 0.040 - 0.080: 520 0.080 - 0.120: 181 0.120 - 0.161: 33 0.161 - 0.201: 6 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA PHE A 687 " pdb=" N PHE A 687 " pdb=" C PHE A 687 " pdb=" CB PHE A 687 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE A 359 " pdb=" CA ILE A 359 " pdb=" CG1 ILE A 359 " pdb=" CG2 ILE A 359 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA VAL A 217 " pdb=" N VAL A 217 " pdb=" C VAL A 217 " pdb=" CB VAL A 217 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 2097 not shown) Planarity restraints: 2487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A1405 " 0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C THR A1405 " -0.067 2.00e-02 2.50e+03 pdb=" O THR A1405 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL A1406 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1408 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C LEU A1408 " 0.063 2.00e-02 2.50e+03 pdb=" O LEU A1408 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA A1409 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 677 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLU A 677 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU A 677 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 678 " -0.019 2.00e-02 2.50e+03 ... (remaining 2484 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 98 2.50 - 3.10: 10878 3.10 - 3.70: 20823 3.70 - 4.30: 29463 4.30 - 4.90: 47286 Nonbonded interactions: 108548 Sorted by model distance: nonbonded pdb=" O2B GTP B1001 " pdb="MG MG B1002 " model vdw 1.901 2.170 nonbonded pdb=" O3G GTP B1001 " pdb="MG MG B1002 " model vdw 2.002 2.170 nonbonded pdb=" OG1 THR B 31 " pdb=" OG1 THR B 48 " model vdw 2.092 3.040 nonbonded pdb=" O1A GTP B1001 " pdb="MG MG B1002 " model vdw 2.103 2.170 nonbonded pdb=" OD1 ASP A1318 " pdb=" NH1 ARG A1345 " model vdw 2.148 3.120 ... (remaining 108543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.40 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.640 Check model and map are aligned: 0.030 Set scattering table: 0.130 Process input model: 35.550 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0320 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 : 0.004 0.039 13967 Z= 0.282 Angle : 0.875 7.940 18915 Z= 0.499 Chirality : 0.048 0.201 2100 Planarity : 0.009 0.097 2487 Dihedral : 14.212 164.342 5207 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.18), residues: 1729 helix: -1.36 (0.15), residues: 817 sheet: -0.48 (0.33), residues: 196 loop : -1.31 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 556 HIS 0.015 0.002 HIS A 63 PHE 0.033 0.003 PHE A 823 TYR 0.029 0.005 TYR A 820 ARG 0.024 0.003 ARG A1208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.5491 (mt) cc_final: -0.6056 (mt) REVERT: A 56 LEU cc_start: 0.6403 (tp) cc_final: 0.6096 (tp) REVERT: A 233 MET cc_start: 0.3090 (mtt) cc_final: 0.2830 (mmm) REVERT: A 421 GLU cc_start: 0.3242 (tp30) cc_final: 0.1670 (mt-10) REVERT: A 437 MET cc_start: 0.7694 (ttt) cc_final: 0.7283 (tmm) REVERT: A 519 ILE cc_start: 0.0065 (mt) cc_final: -0.2672 (mm) REVERT: A 541 ASN cc_start: 0.4731 (t0) cc_final: 0.4304 (t0) REVERT: A 544 LYS cc_start: 0.4106 (mttt) cc_final: 0.3823 (mttt) REVERT: A 555 VAL cc_start: 0.1530 (t) cc_final: 0.1303 (p) REVERT: A 780 ILE cc_start: 0.1706 (mt) cc_final: -0.0004 (mm) REVERT: A 954 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7467 (ttt180) REVERT: A 1210 ASN cc_start: 0.7834 (m-40) cc_final: 0.6916 (t0) REVERT: A 1245 VAL cc_start: 0.7177 (m) cc_final: 0.5161 (m) REVERT: A 1404 MET cc_start: -0.2311 (tpp) cc_final: -0.3653 (tpp) REVERT: A 1513 PHE cc_start: -0.3203 (m-80) cc_final: -0.3444 (m-80) REVERT: B 113 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9123 (tp30) REVERT: B 146 HIS cc_start: 0.7079 (m-70) cc_final: 0.6575 (p90) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.3357 time to fit residues: 143.6809 Evaluate side-chains 178 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 432 GLN A 549 GLN A 756 GLN A1070 GLN A1142 HIS A1526 HIS B 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0463 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13967 Z= 0.254 Angle : 0.713 8.956 18915 Z= 0.383 Chirality : 0.044 0.194 2100 Planarity : 0.005 0.099 2487 Dihedral : 9.384 157.267 1926 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.20 % Allowed : 1.77 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1729 helix: 0.43 (0.18), residues: 835 sheet: -0.65 (0.35), residues: 193 loop : -0.47 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 556 HIS 0.011 0.002 HIS A 63 PHE 0.017 0.002 PHE A 827 TYR 0.018 0.002 TYR A1504 ARG 0.013 0.001 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 216 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.5989 (mt) cc_final: -0.6648 (mt) REVERT: A 56 LEU cc_start: 0.5367 (tp) cc_final: 0.5152 (mt) REVERT: A 432 GLN cc_start: 0.0709 (OUTLIER) cc_final: -0.0191 (pm20) REVERT: A 555 VAL cc_start: 0.0915 (t) cc_final: 0.0568 (p) REVERT: A 602 TYR cc_start: -0.5941 (t80) cc_final: -0.6280 (t80) REVERT: A 780 ILE cc_start: 0.1614 (mt) cc_final: 0.1113 (mm) REVERT: A 954 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7446 (ttt90) REVERT: A 1210 ASN cc_start: 0.7663 (m-40) cc_final: 0.6739 (t0) REVERT: A 1245 VAL cc_start: 0.5516 (m) cc_final: 0.5082 (m) REVERT: A 1288 ILE cc_start: 0.7302 (mt) cc_final: 0.6946 (mm) REVERT: A 1420 VAL cc_start: 0.3808 (p) cc_final: 0.3496 (p) REVERT: B 146 HIS cc_start: 0.7079 (m-70) cc_final: 0.6652 (p90) REVERT: B 171 ASP cc_start: 0.8451 (t70) cc_final: 0.8191 (t0) outliers start: 3 outliers final: 0 residues processed: 219 average time/residue: 0.3064 time to fit residues: 94.2350 Evaluate side-chains 141 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS A 102 GLN A 432 GLN A 583 GLN A1070 GLN A1100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0494 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13967 Z= 0.237 Angle : 0.663 9.549 18915 Z= 0.350 Chirality : 0.043 0.223 2100 Planarity : 0.005 0.079 2487 Dihedral : 9.016 156.157 1926 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.34 % Allowed : 1.64 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1729 helix: 0.80 (0.18), residues: 838 sheet: -0.62 (0.36), residues: 182 loop : -0.40 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 556 HIS 0.008 0.001 HIS A 63 PHE 0.025 0.002 PHE A1244 TYR 0.016 0.002 TYR A1230 ARG 0.006 0.001 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.5587 (mt) cc_final: -0.5984 (mt) REVERT: A 56 LEU cc_start: 0.5377 (tp) cc_final: 0.5067 (mt) REVERT: A 290 TYR cc_start: 0.1759 (m-80) cc_final: 0.1468 (m-80) REVERT: A 432 GLN cc_start: 0.0834 (OUTLIER) cc_final: -0.0036 (pm20) REVERT: A 555 VAL cc_start: 0.0521 (t) cc_final: 0.0197 (p) REVERT: A 602 TYR cc_start: -0.5923 (t80) cc_final: -0.6360 (t80) REVERT: A 954 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7380 (ttt180) REVERT: A 1070 GLN cc_start: -0.1749 (OUTLIER) cc_final: -0.2049 (pp30) REVERT: A 1288 ILE cc_start: 0.7319 (mt) cc_final: 0.6958 (mm) REVERT: A 1398 TYR cc_start: 0.3842 (m-80) cc_final: 0.3554 (m-10) REVERT: A 1420 VAL cc_start: 0.3898 (p) cc_final: 0.3688 (p) REVERT: A 1489 MET cc_start: 0.3066 (tmm) cc_final: 0.2813 (tmm) REVERT: A 1570 ASP cc_start: -0.2632 (m-30) cc_final: -0.3174 (m-30) REVERT: B 146 HIS cc_start: 0.7217 (m-70) cc_final: 0.6615 (p90) REVERT: B 150 HIS cc_start: 0.7009 (m170) cc_final: 0.6605 (m-70) REVERT: B 171 ASP cc_start: 0.8410 (t70) cc_final: 0.8189 (t0) outliers start: 5 outliers final: 1 residues processed: 185 average time/residue: 0.2884 time to fit residues: 76.3020 Evaluate side-chains 136 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 157 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 583 GLN A 999 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0476 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13967 Z= 0.171 Angle : 0.601 8.001 18915 Z= 0.316 Chirality : 0.041 0.220 2100 Planarity : 0.004 0.065 2487 Dihedral : 8.749 153.462 1926 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.20 % Allowed : 2.25 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1729 helix: 1.08 (0.18), residues: 823 sheet: -0.66 (0.35), residues: 196 loop : -0.26 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 556 HIS 0.007 0.001 HIS A 119 PHE 0.014 0.002 PHE A 687 TYR 0.025 0.001 TYR A 433 ARG 0.005 0.000 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 184 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.4955 (tp) cc_final: 0.4666 (mt) REVERT: A 73 VAL cc_start: 0.6505 (p) cc_final: 0.6219 (p) REVERT: A 432 GLN cc_start: 0.0540 (OUTLIER) cc_final: 0.0047 (pm20) REVERT: A 555 VAL cc_start: 0.0057 (t) cc_final: -0.0239 (p) REVERT: A 602 TYR cc_start: -0.5940 (t80) cc_final: -0.6364 (t80) REVERT: A 1288 ILE cc_start: 0.7353 (mt) cc_final: 0.7005 (mm) REVERT: A 1489 MET cc_start: 0.2858 (tmm) cc_final: 0.2609 (tpt) REVERT: B 109 ARG cc_start: 0.7092 (ptt180) cc_final: 0.6535 (ptt-90) REVERT: B 146 HIS cc_start: 0.7247 (m-70) cc_final: 0.6616 (p90) REVERT: B 171 ASP cc_start: 0.8341 (t70) cc_final: 0.8141 (t0) outliers start: 3 outliers final: 0 residues processed: 187 average time/residue: 0.2875 time to fit residues: 76.9678 Evaluate side-chains 137 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 0 optimal weight: 10.9990 chunk 85 optimal weight: 0.0970 chunk 150 optimal weight: 4.9990 chunk 42 optimal weight: 0.0670 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 HIS A 432 GLN A 583 GLN A1095 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0489 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13967 Z= 0.154 Angle : 0.584 7.867 18915 Z= 0.304 Chirality : 0.040 0.172 2100 Planarity : 0.004 0.057 2487 Dihedral : 8.541 151.285 1926 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 0.14 % Allowed : 1.77 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1729 helix: 1.21 (0.18), residues: 815 sheet: -0.71 (0.34), residues: 191 loop : -0.22 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 556 HIS 0.006 0.001 HIS A 119 PHE 0.013 0.001 PHE A 687 TYR 0.022 0.001 TYR A1398 ARG 0.008 0.000 ARG A 853 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.5459 (mt) cc_final: -0.5969 (mt) REVERT: A 56 LEU cc_start: 0.4897 (tp) cc_final: 0.4606 (mt) REVERT: A 73 VAL cc_start: 0.6524 (p) cc_final: 0.6230 (p) REVERT: A 290 TYR cc_start: 0.1924 (m-80) cc_final: 0.1536 (m-80) REVERT: A 555 VAL cc_start: -0.0111 (t) cc_final: -0.0455 (p) REVERT: A 602 TYR cc_start: -0.5947 (t80) cc_final: -0.6382 (t80) REVERT: A 725 ASP cc_start: -0.2786 (t0) cc_final: -0.3433 (t0) REVERT: A 954 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7155 (tpt-90) REVERT: A 1288 ILE cc_start: 0.7113 (mt) cc_final: 0.6775 (mm) REVERT: A 1489 MET cc_start: 0.2740 (tmm) cc_final: 0.2494 (tpt) REVERT: B 146 HIS cc_start: 0.7247 (m-70) cc_final: 0.6593 (p90) REVERT: B 171 ASP cc_start: 0.8329 (t70) cc_final: 0.8119 (t0) outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.2890 time to fit residues: 71.3528 Evaluate side-chains 127 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 167 optimal weight: 30.0000 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 HIS A 432 GLN A 583 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0502 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13967 Z= 0.159 Angle : 0.586 9.667 18915 Z= 0.306 Chirality : 0.041 0.169 2100 Planarity : 0.004 0.051 2487 Dihedral : 8.398 164.513 1926 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 0.20 % Allowed : 1.36 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1729 helix: 1.25 (0.18), residues: 816 sheet: -0.59 (0.34), residues: 199 loop : -0.16 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 556 HIS 0.009 0.001 HIS A 119 PHE 0.011 0.001 PHE A 258 TYR 0.020 0.001 TYR A 433 ARG 0.011 0.000 ARG A1240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.4823 (mt) cc_final: -0.5072 (mt) REVERT: A 56 LEU cc_start: 0.4881 (tp) cc_final: 0.4580 (mt) REVERT: A 73 VAL cc_start: 0.6610 (p) cc_final: 0.6320 (p) REVERT: A 290 TYR cc_start: 0.2398 (m-80) cc_final: 0.2025 (m-80) REVERT: A 432 GLN cc_start: 0.1342 (OUTLIER) cc_final: 0.0919 (pm20) REVERT: A 555 VAL cc_start: 0.0148 (t) cc_final: -0.0281 (p) REVERT: A 602 TYR cc_start: -0.5942 (t80) cc_final: -0.6406 (t80) REVERT: A 716 MET cc_start: -0.4820 (ppp) cc_final: -0.5394 (tmm) REVERT: A 1288 ILE cc_start: 0.7058 (mt) cc_final: 0.6705 (mm) REVERT: A 1489 MET cc_start: 0.2998 (tmm) cc_final: 0.2790 (tpt) REVERT: B 81 TYR cc_start: 0.6975 (m-10) cc_final: 0.6350 (m-80) REVERT: B 146 HIS cc_start: 0.7292 (m-70) cc_final: 0.6596 (p90) outliers start: 3 outliers final: 0 residues processed: 166 average time/residue: 0.2895 time to fit residues: 71.2517 Evaluate side-chains 126 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 94 optimal weight: 30.0000 chunk 140 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 420 HIS A 432 GLN A 575 ASN A 583 GLN A 588 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0565 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13967 Z= 0.283 Angle : 0.671 8.464 18915 Z= 0.354 Chirality : 0.043 0.228 2100 Planarity : 0.005 0.048 2487 Dihedral : 8.427 177.528 1926 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.37 % Rotamer: Outliers : 0.14 % Allowed : 1.16 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1729 helix: 0.98 (0.18), residues: 821 sheet: -0.54 (0.35), residues: 189 loop : -0.37 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 556 HIS 0.009 0.002 HIS A 119 PHE 0.022 0.002 PHE A1424 TYR 0.022 0.002 TYR A1398 ARG 0.014 0.001 ARG A1240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.4395 (mt) cc_final: -0.4631 (mt) REVERT: A 56 LEU cc_start: 0.5465 (tp) cc_final: 0.5248 (mt) REVERT: A 432 GLN cc_start: 0.0924 (OUTLIER) cc_final: 0.0631 (pm20) REVERT: A 555 VAL cc_start: 0.1617 (t) cc_final: 0.0556 (p) REVERT: A 602 TYR cc_start: -0.5850 (t80) cc_final: -0.6361 (t80) REVERT: A 873 VAL cc_start: -0.1125 (t) cc_final: -0.1521 (t) REVERT: B 81 TYR cc_start: 0.7219 (m-10) cc_final: 0.6502 (m-80) REVERT: B 109 ARG cc_start: 0.6968 (ptt180) cc_final: 0.6553 (ppt170) REVERT: B 146 HIS cc_start: 0.7421 (m-70) cc_final: 0.6598 (p90) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.2813 time to fit residues: 62.3411 Evaluate side-chains 110 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 HIS A 432 GLN A 583 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0535 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13967 Z= 0.184 Angle : 0.611 9.851 18915 Z= 0.316 Chirality : 0.041 0.196 2100 Planarity : 0.004 0.043 2487 Dihedral : 8.147 168.937 1926 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.72 % Rotamer: Outliers : 0.14 % Allowed : 0.68 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1729 helix: 1.15 (0.18), residues: 815 sheet: -0.53 (0.35), residues: 194 loop : -0.36 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 66 HIS 0.007 0.001 HIS A 119 PHE 0.017 0.001 PHE A1043 TYR 0.014 0.001 TYR A1046 ARG 0.008 0.000 ARG A1109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.4588 (mt) cc_final: -0.4889 (mt) REVERT: A 56 LEU cc_start: 0.4934 (tp) cc_final: 0.4669 (mt) REVERT: A 432 GLN cc_start: 0.0911 (OUTLIER) cc_final: 0.0598 (pm20) REVERT: A 555 VAL cc_start: 0.0908 (t) cc_final: -0.0023 (p) REVERT: A 602 TYR cc_start: -0.6005 (t80) cc_final: -0.6443 (t80) REVERT: A 873 VAL cc_start: -0.1319 (t) cc_final: -0.1732 (t) REVERT: A 1288 ILE cc_start: 0.6919 (mt) cc_final: 0.6535 (tp) REVERT: B 81 TYR cc_start: 0.7265 (m-10) cc_final: 0.6609 (m-80) REVERT: B 146 HIS cc_start: 0.7391 (m-70) cc_final: 0.6512 (p90) outliers start: 2 outliers final: 0 residues processed: 156 average time/residue: 0.2737 time to fit residues: 62.7385 Evaluate side-chains 119 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS A 432 GLN A 583 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0528 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13967 Z= 0.167 Angle : 0.600 10.135 18915 Z= 0.310 Chirality : 0.041 0.183 2100 Planarity : 0.004 0.044 2487 Dihedral : 7.838 158.305 1926 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 0.14 % Allowed : 0.48 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1729 helix: 1.17 (0.18), residues: 828 sheet: -0.48 (0.36), residues: 194 loop : -0.34 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 66 HIS 0.007 0.001 HIS A 119 PHE 0.016 0.001 PHE A1043 TYR 0.013 0.001 TYR A1046 ARG 0.008 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.4619 (mt) cc_final: -0.4889 (mt) REVERT: A 56 LEU cc_start: 0.4970 (tp) cc_final: 0.4722 (mt) REVERT: A 290 TYR cc_start: 0.2260 (m-80) cc_final: 0.1913 (m-80) REVERT: A 432 GLN cc_start: 0.0845 (OUTLIER) cc_final: 0.0507 (pm20) REVERT: A 555 VAL cc_start: 0.0763 (t) cc_final: -0.0111 (p) REVERT: A 602 TYR cc_start: -0.6002 (t80) cc_final: -0.6379 (t80) REVERT: A 873 VAL cc_start: -0.1589 (t) cc_final: -0.1964 (t) REVERT: A 1570 ASP cc_start: -0.2308 (m-30) cc_final: -0.2665 (m-30) REVERT: B 81 TYR cc_start: 0.7269 (m-10) cc_final: 0.6676 (m-80) REVERT: B 146 HIS cc_start: 0.7425 (m-70) cc_final: 0.6443 (p90) outliers start: 2 outliers final: 0 residues processed: 156 average time/residue: 0.2730 time to fit residues: 62.6117 Evaluate side-chains 122 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 40.0000 chunk 100 optimal weight: 0.0870 chunk 77 optimal weight: 0.4980 chunk 114 optimal weight: 0.2980 chunk 172 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 26 GLN A 432 GLN A 583 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0486 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13967 Z= 0.142 Angle : 0.601 10.580 18915 Z= 0.303 Chirality : 0.041 0.183 2100 Planarity : 0.004 0.044 2487 Dihedral : 7.572 153.847 1926 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 0.20 % Allowed : 0.14 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1729 helix: 1.29 (0.18), residues: 823 sheet: -0.46 (0.36), residues: 196 loop : -0.30 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 66 HIS 0.007 0.001 HIS A 119 PHE 0.016 0.001 PHE A1043 TYR 0.013 0.001 TYR A1046 ARG 0.012 0.000 ARG A1240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: -0.4646 (mt) cc_final: -0.4905 (mt) REVERT: A 56 LEU cc_start: 0.4618 (tp) cc_final: 0.4343 (mt) REVERT: A 290 TYR cc_start: 0.2591 (m-80) cc_final: 0.2229 (m-80) REVERT: A 432 GLN cc_start: 0.0943 (OUTLIER) cc_final: 0.0551 (pm20) REVERT: A 486 LEU cc_start: 0.8215 (tt) cc_final: 0.7730 (tt) REVERT: A 555 VAL cc_start: 0.0365 (t) cc_final: -0.0444 (p) REVERT: A 602 TYR cc_start: -0.6096 (t80) cc_final: -0.6438 (t80) REVERT: B 81 TYR cc_start: 0.7174 (m-10) cc_final: 0.6565 (m-80) REVERT: B 146 HIS cc_start: 0.7380 (m-70) cc_final: 0.6593 (p90) outliers start: 3 outliers final: 0 residues processed: 166 average time/residue: 0.2663 time to fit residues: 64.3417 Evaluate side-chains 132 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 583 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5345 r_free = 0.5345 target = 0.272630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.228614 restraints weight = 99655.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5186 r_free = 0.5186 target = 0.230553 restraints weight = 84307.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5195 r_free = 0.5195 target = 0.232106 restraints weight = 74387.224| |-----------------------------------------------------------------------------| r_work (final): 0.4875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4875 r_free = 0.4875 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5831 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4498 r_free = 0.4498 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7328 | |-----------------------------------------------------------------------------| r_final: 0.4498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0199 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13967 Z= 0.174 Angle : 0.599 10.489 18915 Z= 0.307 Chirality : 0.041 0.176 2100 Planarity : 0.004 0.043 2487 Dihedral : 7.504 152.139 1926 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 0.14 % Allowed : 0.27 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1729 helix: 1.31 (0.18), residues: 823 sheet: -0.48 (0.36), residues: 197 loop : -0.28 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 66 HIS 0.006 0.001 HIS A 119 PHE 0.014 0.001 PHE A1043 TYR 0.022 0.001 TYR A1504 ARG 0.010 0.001 ARG A1240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.62 seconds wall clock time: 57 minutes 32.03 seconds (3452.03 seconds total)