Starting phenix.real_space_refine on Sun Jul 21 10:16:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/07_2024/8p50_17435_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/07_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_17435/07_2024/8p50_17435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/07_2024/8p50_17435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/07_2024/8p50_17435_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p50_17435/07_2024/8p50_17435_neut.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 Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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 - 3.50 Amino acid : False - 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: 5.68 Conformation dependent library (CDL) restraints added in 2.8 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: 2.20 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: 5.72 Time building geometry restraints manager: 6.12 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: 99.47 - 106.40: 345 106.40 - 113.34: 7582 113.34 - 120.28: 5234 120.28 - 127.22: 5638 127.22 - 134.16: 116 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 2.440 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 2.520 ... (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 ========== 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: 1.600 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: 0.480 Check model and map are aligned: 0.020 Set scattering table: 0.130 Process input model: 42.010 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.300 ------------------------------------------------------------------------------- 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 : 1.533 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: 0.3479 time to fit residues: 151.0711 Evaluate side-chains 178 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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: 10.0000 chunk 131 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 509 GLN A 549 GLN A 756 GLN A1070 GLN A1142 HIS A1526 HIS B 52 ASN B 128 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0469 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13967 Z= 0.253 Angle : 0.702 8.935 18915 Z= 0.376 Chirality : 0.044 0.190 2100 Planarity : 0.005 0.072 2487 Dihedral : 9.343 157.770 1926 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.14 % Allowed : 2.05 % Favored : 97.82 % 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: -0.21 (0.20), residues: 1729 helix: 0.40 (0.18), residues: 833 sheet: -0.50 (0.34), residues: 198 loop : -0.52 (0.24), residues: 698 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 0.018 0.002 PHE A 827 TYR 0.017 0.002 TYR A1046 ARG 0.008 0.001 ARG A1278 *********************** 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 221 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 1.485 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: -0.5977 (mt) cc_final: -0.6596 (mt) REVERT: A 56 LEU cc_start: 0.5317 (tp) cc_final: 0.5085 (mt) REVERT: A 432 GLN cc_start: 0.1032 (OUTLIER) cc_final: -0.0243 (pm20) REVERT: A 602 TYR cc_start: -0.5824 (t80) cc_final: -0.6154 (t80) REVERT: A 780 ILE cc_start: 0.1461 (mt) cc_final: 0.1034 (mm) REVERT: A 954 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7438 (ttt90) REVERT: A 1210 ASN cc_start: 0.7670 (m-40) cc_final: 0.6714 (t0) REVERT: A 1245 VAL cc_start: 0.5525 (m) cc_final: 0.5088 (m) REVERT: A 1288 ILE cc_start: 0.7256 (mt) cc_final: 0.6929 (tp) REVERT: B 146 HIS cc_start: 0.7094 (m-70) cc_final: 0.6651 (p90) REVERT: B 171 ASP cc_start: 0.8540 (t70) cc_final: 0.8280 (t0) outliers start: 2 outliers final: 0 residues processed: 221 average time/residue: 0.3168 time to fit residues: 99.2945 Evaluate side-chains 134 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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: 4.9990 chunk 48 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 509 GLN ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 GLN A1100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0502 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13967 Z= 0.239 Angle : 0.660 8.723 18915 Z= 0.348 Chirality : 0.042 0.199 2100 Planarity : 0.004 0.054 2487 Dihedral : 8.886 168.160 1926 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.14 % Allowed : 2.05 % Favored : 97.82 % 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: 0.14 (0.20), residues: 1729 helix: 0.78 (0.18), residues: 838 sheet: -0.58 (0.35), residues: 192 loop : -0.42 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 556 HIS 0.008 0.001 HIS A 63 PHE 0.016 0.002 PHE B 63 TYR 0.032 0.002 TYR A 433 ARG 0.010 0.001 ARG A1294 *********************** 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 175 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 1.440 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: A 56 LEU cc_start: 0.5281 (tp) cc_final: 0.4978 (mt) REVERT: A 432 GLN cc_start: 0.0588 (OUTLIER) cc_final: -0.0477 (pm20) REVERT: A 602 TYR cc_start: -0.5775 (t80) cc_final: -0.6188 (t80) REVERT: A 954 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7441 (ttt180) REVERT: A 1288 ILE cc_start: 0.7273 (mt) cc_final: 0.6944 (mm) REVERT: B 146 HIS cc_start: 0.7222 (m-70) cc_final: 0.6596 (p90) REVERT: B 171 ASP cc_start: 0.8426 (t70) cc_final: 0.8219 (t0) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.2756 time to fit residues: 68.8880 Evaluate side-chains 128 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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: 6.9990 chunk 118 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 509 GLN A 583 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0471 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13967 Z= 0.162 Angle : 0.592 7.931 18915 Z= 0.309 Chirality : 0.041 0.253 2100 Planarity : 0.004 0.047 2487 Dihedral : 8.501 175.912 1926 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.14 % Allowed : 2.25 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.21), residues: 1729 helix: 1.15 (0.18), residues: 822 sheet: -0.52 (0.36), residues: 192 loop : -0.29 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 556 HIS 0.008 0.001 HIS A 63 PHE 0.014 0.001 PHE A 687 TYR 0.017 0.001 TYR A 768 ARG 0.006 0.000 ARG A 853 *********************** 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 181 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 1.422 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: -0.4945 (mt) cc_final: -0.5404 (mt) REVERT: A 56 LEU cc_start: 0.4828 (tp) cc_final: 0.4501 (mt) REVERT: A 432 GLN cc_start: 0.0739 (OUTLIER) cc_final: 0.0020 (pm20) REVERT: A 602 TYR cc_start: -0.5803 (t80) cc_final: -0.6213 (t80) REVERT: A 1288 ILE cc_start: 0.7287 (mt) cc_final: 0.6966 (mm) REVERT: B 109 ARG cc_start: 0.7062 (ptt180) cc_final: 0.6442 (ptt-90) REVERT: B 146 HIS cc_start: 0.7206 (m-70) cc_final: 0.6567 (p90) REVERT: B 150 HIS cc_start: 0.6949 (m170) cc_final: 0.6570 (m-70) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.2836 time to fit residues: 74.7407 Evaluate side-chains 130 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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: 0.0980 chunk 94 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 142 optimal weight: 0.0470 chunk 115 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 509 GLN A 583 GLN A1526 HIS A1583 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0450 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13967 Z= 0.138 Angle : 0.564 8.228 18915 Z= 0.290 Chirality : 0.040 0.176 2100 Planarity : 0.004 0.046 2487 Dihedral : 7.964 162.148 1926 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.14 % Allowed : 1.43 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: 0.62 (0.21), residues: 1729 helix: 1.32 (0.18), residues: 820 sheet: -0.50 (0.35), residues: 193 loop : -0.29 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 556 HIS 0.007 0.001 HIS A 63 PHE 0.015 0.001 PHE A1043 TYR 0.021 0.001 TYR A1398 ARG 0.008 0.000 ARG A1351 *********************** 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 183 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 1.575 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: A 48 LEU cc_start: -0.4776 (mt) cc_final: -0.5715 (mt) REVERT: A 56 LEU cc_start: 0.4491 (tp) cc_final: 0.4180 (mt) REVERT: A 432 GLN cc_start: 0.0997 (OUTLIER) cc_final: 0.0780 (pm20) REVERT: A 602 TYR cc_start: -0.5798 (t80) cc_final: -0.6212 (t80) REVERT: A 1489 MET cc_start: 0.0665 (tpt) cc_final: 0.0447 (tpt) REVERT: B 109 ARG cc_start: 0.6849 (ptt180) cc_final: 0.6460 (ptt-90) REVERT: B 110 MET cc_start: 0.7333 (mmt) cc_final: 0.6807 (mmm) REVERT: B 146 HIS cc_start: 0.7199 (m-70) cc_final: 0.6569 (p90) outliers start: 2 outliers final: 0 residues processed: 183 average time/residue: 0.2896 time to fit residues: 75.4534 Evaluate side-chains 139 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 167 optimal weight: 30.0000 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.0270 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 63 HIS A 418 ASN A 420 HIS A 432 GLN A 583 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0502 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13967 Z= 0.168 Angle : 0.576 6.743 18915 Z= 0.304 Chirality : 0.040 0.166 2100 Planarity : 0.004 0.046 2487 Dihedral : 7.723 154.708 1926 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.20 % Allowed : 1.71 % 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: 0.72 (0.21), residues: 1729 helix: 1.43 (0.18), residues: 808 sheet: -0.40 (0.36), residues: 185 loop : -0.26 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 556 HIS 0.009 0.001 HIS A 119 PHE 0.012 0.001 PHE A 30 TYR 0.021 0.001 TYR A1398 ARG 0.012 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 171 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.595 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 56 LEU cc_start: 0.4950 (tp) cc_final: 0.4644 (mt) REVERT: A 432 GLN cc_start: 0.1590 (OUTLIER) cc_final: 0.1218 (pm20) REVERT: A 506 PHE cc_start: -0.4885 (t80) cc_final: -0.5141 (t80) REVERT: A 602 TYR cc_start: -0.5795 (t80) cc_final: -0.6255 (t80) REVERT: A 725 ASP cc_start: -0.2415 (t0) cc_final: -0.2713 (t0) REVERT: B 109 ARG cc_start: 0.7020 (ptt180) cc_final: 0.6414 (ptt-90) REVERT: B 146 HIS cc_start: 0.7310 (m-70) cc_final: 0.6636 (p90) outliers start: 3 outliers final: 0 residues processed: 171 average time/residue: 0.2696 time to fit residues: 67.0741 Evaluate side-chains 130 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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: 5.9990 chunk 18 optimal weight: 10.0000 chunk 95 optimal weight: 0.2980 chunk 122 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 688 HIS A1583 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0483 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13967 Z= 0.137 Angle : 0.571 8.733 18915 Z= 0.292 Chirality : 0.040 0.189 2100 Planarity : 0.004 0.046 2487 Dihedral : 7.523 151.191 1926 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.65 % 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: 0.81 (0.21), residues: 1729 helix: 1.45 (0.18), residues: 817 sheet: -0.30 (0.36), residues: 185 loop : -0.20 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 556 HIS 0.008 0.001 HIS A 119 PHE 0.046 0.001 PHE A1424 TYR 0.018 0.001 TYR A1398 ARG 0.013 0.000 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 172 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 1.524 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: -0.4612 (mt) cc_final: -0.5582 (mt) REVERT: A 56 LEU cc_start: 0.4489 (tp) cc_final: 0.4151 (mt) REVERT: A 432 GLN cc_start: 0.1518 (OUTLIER) cc_final: 0.1200 (pm20) REVERT: A 602 TYR cc_start: -0.5898 (t80) cc_final: -0.6251 (t80) REVERT: A 725 ASP cc_start: -0.2759 (t0) cc_final: -0.3358 (t0) REVERT: A 1398 TYR cc_start: 0.2952 (m-10) cc_final: 0.2641 (m-10) REVERT: B 146 HIS cc_start: 0.7314 (m-70) cc_final: 0.6589 (p90) outliers start: 2 outliers final: 0 residues processed: 172 average time/residue: 0.2691 time to fit residues: 67.2722 Evaluate side-chains 130 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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: 10.0000 chunk 99 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 0.0770 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 overall best weight: 3.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 GLN A 420 HIS A 432 GLN A 583 GLN ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1526 HIS A1583 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0569 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13967 Z= 0.279 Angle : 0.654 9.511 18915 Z= 0.347 Chirality : 0.042 0.168 2100 Planarity : 0.004 0.046 2487 Dihedral : 7.704 151.485 1926 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 0.14 % Allowed : 0.89 % Favored : 98.98 % 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: 1.28 (0.18), residues: 810 sheet: -0.33 (0.36), residues: 182 loop : -0.31 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 556 HIS 0.007 0.001 HIS A 119 PHE 0.021 0.002 PHE A 887 TYR 0.021 0.002 TYR A1398 ARG 0.007 0.001 ARG A 853 *********************** 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 149 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.550 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: A 48 LEU cc_start: -0.4493 (mt) cc_final: -0.4846 (mt) REVERT: A 56 LEU cc_start: 0.5145 (tp) cc_final: 0.4919 (mt) REVERT: A 432 GLN cc_start: 0.1304 (OUTLIER) cc_final: 0.0811 (pm20) REVERT: A 602 TYR cc_start: -0.5617 (t80) cc_final: -0.6085 (t80) REVERT: A 873 VAL cc_start: -0.1044 (t) cc_final: -0.1477 (t) REVERT: A 954 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.7309 (ttm-80) REVERT: A 1424 PHE cc_start: 0.4696 (m-10) cc_final: 0.0940 (m-10) REVERT: B 81 TYR cc_start: 0.7116 (m-10) cc_final: 0.6552 (m-80) REVERT: B 109 ARG cc_start: 0.7106 (ptt180) cc_final: 0.6466 (ptt-90) REVERT: B 146 HIS cc_start: 0.7385 (m-70) cc_final: 0.6635 (p-80) outliers start: 2 outliers final: 0 residues processed: 149 average time/residue: 0.2689 time to fit residues: 58.7502 Evaluate side-chains 108 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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: 0.3980 chunk 145 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 140 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 418 ASN A 432 GLN A 583 GLN A1095 GLN A1218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0505 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13967 Z= 0.136 Angle : 0.578 9.995 18915 Z= 0.297 Chirality : 0.040 0.187 2100 Planarity : 0.004 0.046 2487 Dihedral : 7.548 152.752 1926 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 0.27 % Allowed : 0.14 % 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: 0.83 (0.21), residues: 1729 helix: 1.50 (0.19), residues: 812 sheet: -0.21 (0.36), residues: 185 loop : -0.24 (0.24), residues: 732 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 0.013 0.001 PHE A1424 TYR 0.013 0.001 TYR A1398 ARG 0.012 0.000 ARG A1240 *********************** 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 168 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.634 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: A 48 LEU cc_start: -0.4669 (mt) cc_final: -0.5147 (mt) REVERT: A 56 LEU cc_start: 0.4697 (tp) cc_final: 0.4436 (mt) REVERT: A 73 VAL cc_start: 0.6616 (p) cc_final: 0.6332 (p) REVERT: A 432 GLN cc_start: 0.1361 (OUTLIER) cc_final: 0.1054 (pm20) REVERT: A 602 TYR cc_start: -0.5896 (t80) cc_final: -0.6237 (t80) REVERT: A 725 ASP cc_start: -0.2824 (t0) cc_final: -0.3063 (t0) REVERT: A 954 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7215 (mtp180) REVERT: A 1062 MET cc_start: -0.2611 (tpp) cc_final: -0.2831 (tpp) REVERT: B 81 TYR cc_start: 0.7136 (m-10) cc_final: 0.6451 (m-80) REVERT: B 109 ARG cc_start: 0.7528 (ptt180) cc_final: 0.6966 (ptt90) REVERT: B 146 HIS cc_start: 0.7411 (m-70) cc_final: 0.6600 (p-80) outliers start: 4 outliers final: 1 residues processed: 168 average time/residue: 0.2646 time to fit residues: 65.8724 Evaluate side-chains 123 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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: 30.0000 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 114 optimal weight: 30.0000 chunk 172 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 583 GLN ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0562 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13967 Z= 0.264 Angle : 0.651 10.193 18915 Z= 0.343 Chirality : 0.042 0.214 2100 Planarity : 0.004 0.047 2487 Dihedral : 7.721 155.055 1926 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.73 % 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: 1.11 (0.18), residues: 823 sheet: -0.40 (0.36), residues: 182 loop : -0.39 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 556 HIS 0.007 0.001 HIS A 119 PHE 0.025 0.002 PHE A 30 TYR 0.038 0.002 TYR A1235 ARG 0.014 0.001 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 148 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.495 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: A 48 LEU cc_start: -0.4524 (mt) cc_final: -0.4809 (mt) REVERT: A 56 LEU cc_start: 0.5187 (tp) cc_final: 0.4987 (mt) REVERT: A 432 GLN cc_start: 0.1147 (OUTLIER) cc_final: 0.0694 (pm20) REVERT: A 486 LEU cc_start: 0.8079 (tt) cc_final: 0.7532 (mt) REVERT: A 873 VAL cc_start: -0.1133 (t) cc_final: -0.1545 (t) REVERT: A 1424 PHE cc_start: 0.4279 (m-10) cc_final: 0.1103 (m-10) REVERT: B 81 TYR cc_start: 0.7214 (m-10) cc_final: 0.6626 (m-80) REVERT: B 121 LEU cc_start: 0.6737 (tt) cc_final: 0.6142 (mt) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.2582 time to fit residues: 57.2921 Evaluate side-chains 108 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 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: 6.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 137 optimal weight: 0.3980 chunk 57 optimal weight: 0.0020 chunk 141 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 583 GLN ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5352 r_free = 0.5352 target = 0.271984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.228385 restraints weight = 100712.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5175 r_free = 0.5175 target = 0.229926 restraints weight = 85819.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5193 r_free = 0.5193 target = 0.232348 restraints weight = 77204.949| |-----------------------------------------------------------------------------| r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4867 r_free = 0.4867 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5831 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4491 r_free = 0.4491 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7419 | |-----------------------------------------------------------------------------| r_final: 0.4491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0265 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13967 Z= 0.165 Angle : 0.586 10.179 18915 Z= 0.304 Chirality : 0.041 0.203 2100 Planarity : 0.004 0.046 2487 Dihedral : 7.642 156.796 1926 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 0.14 % Allowed : 0.20 % 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: 0.56 (0.21), residues: 1729 helix: 1.24 (0.18), residues: 822 sheet: -0.40 (0.36), residues: 188 loop : -0.33 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 556 HIS 0.007 0.001 HIS A 119 PHE 0.013 0.001 PHE A 30 TYR 0.026 0.001 TYR A1235 ARG 0.010 0.000 ARG A1240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3151.79 seconds wall clock time: 56 minutes 14.51 seconds (3374.51 seconds total)