Starting phenix.real_space_refine on Fri Dec 8 19:30:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/12_2023/7vlr_32024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/12_2023/7vlr_32024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/12_2023/7vlr_32024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/12_2023/7vlr_32024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/12_2023/7vlr_32024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/12_2023/7vlr_32024.pdb" } resolution = 3.4 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= 0.007 sd= 0.131 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 5 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5833 2.51 5 N 1493 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9003 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9003 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'Y01': 1} Classifications: {'peptide': 1145, 'undetermined': 5} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 33, 'TRANS': 1111, None: 5} Not linked: pdbres="MET A1545 " pdbres="Y01 A1601 " Not linked: pdbres="Y01 A1601 " pdbres="ADP A1602 " Not linked: pdbres="ADP A1602 " pdbres=" MG A1603 " Not linked: pdbres=" MG A1603 " pdbres=" MG A1604 " Not linked: pdbres=" MG A1604 " pdbres="ATP A1605 " Chain breaks: 5 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Time building chain proxies: 5.29, per 1000 atoms: 0.59 Number of scatterers: 9003 At special positions: 0 Unit cell: (72.27, 90.666, 135.342, 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 46 16.00 P 5 15.00 Mg 2 11.99 O 1624 8.00 N 1493 7.00 C 5833 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=0, symmetry=0 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 72.2% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 256 through 278 removed outlier: 3.518A pdb=" N ASN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 327 removed outlier: 5.870A pdb=" N ARG A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix removed outlier: 3.505A pdb=" N LEU A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.740A pdb=" N ASN A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 395 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.562A pdb=" N VAL A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 429 through 450 Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 451 through 462 removed outlier: 4.207A pdb=" N VAL A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 505 removed outlier: 5.915A pdb=" N LYS A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 559 Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 564 through 607 Proline residue: A 581 - end of helix removed outlier: 4.305A pdb=" N LEU A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 761 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 785 through 791 removed outlier: 4.482A pdb=" N ASP A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 839 through 850 Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 868 through 874 removed outlier: 4.046A pdb=" N THR A 873 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 899 through 911 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 988 through 1016 Processing helix chain 'A' and resid 1029 through 1075 removed outlier: 4.071A pdb=" N VAL A1053 " --> pdb=" O THR A1049 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1074 " --> pdb=" O ASN A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.735A pdb=" N PHE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1102 removed outlier: 4.151A pdb=" N ARG A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A1095 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1128 Processing helix chain 'A' and resid 1130 through 1176 removed outlier: 3.741A pdb=" N ALA A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) Proline residue: A1137 - end of helix Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1186 through 1238 removed outlier: 3.578A pdb=" N SER A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1282 removed outlier: 3.563A pdb=" N VAL A1244 " --> pdb=" O ASN A1240 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A1245 " --> pdb=" O SER A1241 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A1275 " --> pdb=" O GLN A1271 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A1282 " --> pdb=" O VAL A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1355 removed outlier: 3.950A pdb=" N PHE A1355 " --> pdb=" O LEU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1384 removed outlier: 3.523A pdb=" N ARG A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1432 through 1435 Processing helix chain 'A' and resid 1439 through 1443 removed outlier: 3.618A pdb=" N GLU A1443 " --> pdb=" O GLU A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1462 removed outlier: 4.218A pdb=" N ARG A1461 " --> pdb=" O ARG A1457 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A1462 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1491 removed outlier: 3.729A pdb=" N ILE A1482 " --> pdb=" O ALA A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1507 removed outlier: 4.086A pdb=" N ILE A1506 " --> pdb=" O ARG A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1532 Processing helix chain 'A' and resid 1535 through 1545 Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 692 removed outlier: 6.919A pdb=" N PHE A 675 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 685 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY A 673 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 687 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 671 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A 689 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS A 669 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 691 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY A 673 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 722 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE A 675 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR A 720 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 748 through 751 removed outlier: 6.592A pdb=" N VAL A 829 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL A 865 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A 831 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A 697 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 878 " --> pdb=" O GLU A 889 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU A 889 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA A 880 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1328 through 1332 removed outlier: 5.367A pdb=" N VAL A1328 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A1313 " --> pdb=" O ASP A1363 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP A1363 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A1315 " --> pdb=" O ILE A1361 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE A1361 " --> pdb=" O VAL A1315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1386 through 1388 removed outlier: 6.890A pdb=" N SER A1386 " --> pdb=" O ILE A1467 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ASP A1469 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A1388 " --> pdb=" O ASP A1469 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A1466 " --> pdb=" O VAL A1497 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE A1499 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET A1468 " --> pdb=" O ILE A1499 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A1338 " --> pdb=" O THR A1498 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS A1337 " --> pdb=" O LEU A1511 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE A1513 " --> pdb=" O LYS A1337 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLY A1339 " --> pdb=" O ILE A1513 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N MET A1515 " --> pdb=" O GLY A1339 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N CYS A1341 " --> pdb=" O MET A1515 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A1512 " --> pdb=" O TYR A1523 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR A1523 " --> pdb=" O VAL A1512 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A1514 " --> pdb=" O LEU A1521 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1397 through 1398 626 hydrogen bonds defined for protein. 1845 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: 2.94 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1844 1.33 - 1.45: 2044 1.45 - 1.57: 5217 1.57 - 1.70: 6 1.70 - 1.82: 74 Bond restraints: 9185 Sorted by residual: bond pdb=" CAY Y01 A1601 " pdb=" OAW Y01 A1601 " ideal model delta sigma weight residual 1.332 1.461 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" CAX Y01 A1601 " pdb=" OAH Y01 A1601 " ideal model delta sigma weight residual 1.248 1.330 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CA PHE A1281 " pdb=" C PHE A1281 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.41e-02 5.03e+03 6.75e+00 bond pdb=" CA VAL A1278 " pdb=" CB VAL A1278 " ideal model delta sigma weight residual 1.540 1.511 0.029 1.25e-02 6.40e+03 5.47e+00 bond pdb=" CA SER A1280 " pdb=" C SER A1280 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.30e-02 5.92e+03 4.42e+00 ... (remaining 9180 not shown) Histogram of bond angle deviations from ideal: 99.53 - 107.48: 324 107.48 - 115.44: 5669 115.44 - 123.40: 6266 123.40 - 131.36: 206 131.36 - 139.31: 25 Bond angle restraints: 12490 Sorted by residual: angle pdb=" C5' ATP A1605 " pdb=" C4' ATP A1605 " pdb=" O4' ATP A1605 " ideal model delta sigma weight residual 109.53 103.39 6.14 1.44e+00 4.84e-01 1.82e+01 angle pdb=" N9 ATP A1605 " pdb=" C1' ATP A1605 " pdb=" O4' ATP A1605 " ideal model delta sigma weight residual 108.36 103.86 4.50 1.26e+00 6.30e-01 1.28e+01 angle pdb=" O2A ATP A1605 " pdb=" PA ATP A1605 " pdb=" O5' ATP A1605 " ideal model delta sigma weight residual 108.07 117.11 -9.04 2.65e+00 1.42e-01 1.16e+01 angle pdb=" C3' ATP A1605 " pdb=" C4' ATP A1605 " pdb=" C5' ATP A1605 " ideal model delta sigma weight residual 115.19 109.26 5.93 1.76e+00 3.23e-01 1.14e+01 angle pdb=" C LEU A1282 " pdb=" N THR A1283 " pdb=" CA THR A1283 " ideal model delta sigma weight residual 122.06 115.89 6.17 1.86e+00 2.89e-01 1.10e+01 ... (remaining 12485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.66: 5348 27.66 - 55.33: 150 55.33 - 82.99: 17 82.99 - 110.65: 1 110.65 - 138.31: 1 Dihedral angle restraints: 5517 sinusoidal: 2185 harmonic: 3332 Sorted by residual: dihedral pdb=" O2A ADP A1602 " pdb=" O3A ADP A1602 " pdb=" PA ADP A1602 " pdb=" PB ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 78.31 -138.31 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" O1B ADP A1602 " pdb=" O3A ADP A1602 " pdb=" PB ADP A1602 " pdb=" PA ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 17.53 -77.53 1 2.00e+01 2.50e-03 1.88e+01 dihedral pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" N GLU A 417 " pdb=" CA GLU A 417 " ideal model delta harmonic sigma weight residual 180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1300 0.061 - 0.121: 168 0.121 - 0.182: 20 0.182 - 0.242: 3 0.242 - 0.303: 3 Chirality restraints: 1494 Sorted by residual: chirality pdb=" C4' ATP A1605 " pdb=" C3' ATP A1605 " pdb=" C5' ATP A1605 " pdb=" O4' ATP A1605 " both_signs ideal model delta sigma weight residual False -2.49 -2.80 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA PHE A1281 " pdb=" N PHE A1281 " pdb=" C PHE A1281 " pdb=" CB PHE A1281 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CBB Y01 A1601 " pdb=" CAC Y01 A1601 " pdb=" CAO Y01 A1601 " pdb=" CBE Y01 A1601 " both_signs ideal model delta sigma weight residual False 2.58 2.33 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1491 not shown) Planarity restraints: 1527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 851 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C ILE A 851 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 851 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 852 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 848 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C GLN A 848 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN A 848 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU A 849 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 543 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO A 544 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 544 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 544 " -0.021 5.00e-02 4.00e+02 ... (remaining 1524 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 32 2.62 - 3.19: 8467 3.19 - 3.76: 14100 3.76 - 4.33: 19747 4.33 - 4.90: 32483 Nonbonded interactions: 74829 Sorted by model distance: nonbonded pdb=" OE1 GLN A 753 " pdb="MG MG A1603 " model vdw 2.052 2.170 nonbonded pdb=" OG SER A 708 " pdb="MG MG A1603 " model vdw 2.072 2.170 nonbonded pdb=" O1B ADP A1602 " pdb="MG MG A1604 " model vdw 2.121 2.170 nonbonded pdb=" NZ LYS A 503 " pdb=" OE2 GLU A 508 " model vdw 2.352 2.520 nonbonded pdb=" OE2 GLU A 717 " pdb=" NH2 ARG A1182 " model vdw 2.356 2.520 ... (remaining 74824 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 2.250 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 27.120 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 0.129 9185 Z= 0.239 Angle : 0.607 9.042 12490 Z= 0.316 Chirality : 0.044 0.303 1494 Planarity : 0.004 0.037 1527 Dihedral : 12.838 138.314 3359 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.94 % Allowed : 3.96 % Favored : 95.10 % 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: 1.47 (0.25), residues: 1133 helix: 1.66 (0.19), residues: 747 sheet: -0.21 (0.61), residues: 60 loop : -0.31 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 423 HIS 0.003 0.001 HIS A1065 PHE 0.006 0.001 PHE A 424 TYR 0.007 0.001 TYR A1523 ARG 0.002 0.000 ARG A1413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 232 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 238 average time/residue: 0.2578 time to fit residues: 82.8438 Evaluate side-chains 108 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1130 time to fit residues: 1.7907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 0.0040 chunk 54 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 841 HIS ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9185 Z= 0.197 Angle : 0.562 8.956 12490 Z= 0.283 Chirality : 0.040 0.180 1494 Planarity : 0.004 0.041 1527 Dihedral : 8.036 133.774 1335 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.88 % Allowed : 11.57 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.64 (0.25), residues: 1133 helix: 2.47 (0.18), residues: 757 sheet: 0.44 (0.64), residues: 65 loop : 0.28 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 980 HIS 0.004 0.001 HIS A 845 PHE 0.011 0.001 PHE A 854 TYR 0.012 0.001 TYR A1009 ARG 0.004 0.000 ARG A1213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.078 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 133 average time/residue: 0.1871 time to fit residues: 36.9233 Evaluate side-chains 104 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0924 time to fit residues: 3.1824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 104 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 ASN A1311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9185 Z= 0.171 Angle : 0.501 8.086 12490 Z= 0.250 Chirality : 0.039 0.186 1494 Planarity : 0.003 0.050 1527 Dihedral : 7.604 136.078 1335 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.56 % Allowed : 13.87 % Favored : 84.57 % 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: 3.02 (0.25), residues: 1133 helix: 2.76 (0.19), residues: 760 sheet: 0.90 (0.59), residues: 75 loop : 0.29 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 980 HIS 0.004 0.001 HIS A1066 PHE 0.010 0.001 PHE A 293 TYR 0.008 0.001 TYR A1523 ARG 0.002 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.028 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 124 average time/residue: 0.1874 time to fit residues: 34.1931 Evaluate side-chains 98 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0881 time to fit residues: 2.7004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0670 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9185 Z= 0.178 Angle : 0.511 10.185 12490 Z= 0.249 Chirality : 0.039 0.189 1494 Planarity : 0.003 0.051 1527 Dihedral : 7.418 140.438 1335 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.56 % Allowed : 14.49 % Favored : 83.94 % 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: 3.03 (0.25), residues: 1133 helix: 2.75 (0.19), residues: 765 sheet: 1.01 (0.59), residues: 75 loop : 0.27 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 980 HIS 0.004 0.001 HIS A 278 PHE 0.010 0.001 PHE A 569 TYR 0.009 0.001 TYR A1523 ARG 0.003 0.000 ARG A1263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.089 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 111 average time/residue: 0.1725 time to fit residues: 29.0477 Evaluate side-chains 94 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0968 time to fit residues: 2.4205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.0000 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9185 Z= 0.137 Angle : 0.477 7.588 12490 Z= 0.236 Chirality : 0.038 0.190 1494 Planarity : 0.003 0.053 1527 Dihedral : 7.126 137.186 1335 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.31 % Allowed : 16.89 % Favored : 82.79 % 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: 3.17 (0.25), residues: 1133 helix: 2.85 (0.18), residues: 765 sheet: 1.27 (0.59), residues: 75 loop : 0.26 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 432 HIS 0.003 0.001 HIS A1066 PHE 0.008 0.001 PHE A1149 TYR 0.015 0.001 TYR A1009 ARG 0.004 0.000 ARG A1263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 1.750 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 108 average time/residue: 0.2318 time to fit residues: 39.0017 Evaluate side-chains 91 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0854 time to fit residues: 1.5131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9185 Z= 0.181 Angle : 0.513 10.090 12490 Z= 0.247 Chirality : 0.039 0.188 1494 Planarity : 0.003 0.056 1527 Dihedral : 7.034 136.972 1335 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.83 % Allowed : 17.73 % Favored : 81.44 % 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: 3.11 (0.25), residues: 1133 helix: 2.78 (0.18), residues: 767 sheet: 1.51 (0.60), residues: 75 loop : 0.22 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1260 HIS 0.004 0.001 HIS A1065 PHE 0.010 0.001 PHE A1149 TYR 0.010 0.001 TYR A1205 ARG 0.003 0.000 ARG A1263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.024 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 98 average time/residue: 0.1847 time to fit residues: 27.4026 Evaluate side-chains 87 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0957 time to fit residues: 1.9185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9185 Z= 0.269 Angle : 0.552 8.001 12490 Z= 0.272 Chirality : 0.041 0.209 1494 Planarity : 0.003 0.055 1527 Dihedral : 7.292 143.101 1335 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.36 % Allowed : 17.94 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.94 (0.25), residues: 1133 helix: 2.62 (0.19), residues: 767 sheet: 1.50 (0.60), residues: 75 loop : 0.25 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1260 HIS 0.003 0.001 HIS A1001 PHE 0.011 0.001 PHE A 424 TYR 0.014 0.001 TYR A1523 ARG 0.003 0.000 ARG A1112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 1.077 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 0.1822 time to fit residues: 28.6581 Evaluate side-chains 91 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0828 time to fit residues: 2.6088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.0010 chunk 106 optimal weight: 0.5980 chunk 96 optimal weight: 0.3980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9185 Z= 0.153 Angle : 0.517 12.087 12490 Z= 0.248 Chirality : 0.039 0.198 1494 Planarity : 0.003 0.056 1527 Dihedral : 6.974 133.148 1335 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.31 % Allowed : 19.08 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.13 (0.25), residues: 1133 helix: 2.77 (0.18), residues: 765 sheet: 1.67 (0.61), residues: 75 loop : 0.27 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 432 HIS 0.003 0.001 HIS A1066 PHE 0.007 0.001 PHE A1149 TYR 0.009 0.001 TYR A1523 ARG 0.004 0.000 ARG A1263 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 1.089 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.1770 time to fit residues: 25.5315 Evaluate side-chains 83 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0876 time to fit residues: 1.5446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 109 optimal weight: 0.7980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9185 Z= 0.180 Angle : 0.518 8.122 12490 Z= 0.252 Chirality : 0.039 0.198 1494 Planarity : 0.003 0.057 1527 Dihedral : 6.855 129.255 1335 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.73 % Allowed : 18.67 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.10 (0.25), residues: 1133 helix: 2.70 (0.18), residues: 769 sheet: 1.70 (0.60), residues: 75 loop : 0.38 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 423 HIS 0.004 0.001 HIS A1001 PHE 0.011 0.001 PHE A 312 TYR 0.016 0.001 TYR A1009 ARG 0.003 0.000 ARG A1263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.957 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.1751 time to fit residues: 24.4698 Evaluate side-chains 88 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0813 time to fit residues: 1.8623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9185 Z= 0.234 Angle : 0.548 7.809 12490 Z= 0.267 Chirality : 0.041 0.202 1494 Planarity : 0.003 0.055 1527 Dihedral : 6.933 129.046 1335 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.21 % Allowed : 19.08 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.01 (0.25), residues: 1133 helix: 2.63 (0.19), residues: 768 sheet: 1.69 (0.60), residues: 75 loop : 0.34 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 423 HIS 0.003 0.001 HIS A1065 PHE 0.014 0.001 PHE A 312 TYR 0.014 0.001 TYR A1205 ARG 0.002 0.000 ARG A1263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.088 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.1908 time to fit residues: 24.2716 Evaluate side-chains 78 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.094563 restraints weight = 14522.602| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.47 r_work: 0.3012 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9185 Z= 0.188 Angle : 0.528 11.647 12490 Z= 0.255 Chirality : 0.039 0.200 1494 Planarity : 0.003 0.055 1527 Dihedral : 6.854 126.036 1335 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.31 % Allowed : 19.60 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.04 (0.25), residues: 1133 helix: 2.68 (0.18), residues: 768 sheet: 1.71 (0.60), residues: 75 loop : 0.27 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 423 HIS 0.003 0.001 HIS A1001 PHE 0.011 0.001 PHE A 312 TYR 0.010 0.001 TYR A1523 ARG 0.005 0.000 ARG A1517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.97 seconds wall clock time: 34 minutes 49.07 seconds (2089.07 seconds total)