Starting phenix.real_space_refine on Thu Mar 14 13:20:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/03_2024/7vlr_32024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/03_2024/7vlr_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_32024/03_2024/7vlr_32024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/03_2024/7vlr_32024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/03_2024/7vlr_32024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlr_32024/03_2024/7vlr_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-dev-5265/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: 5.26, per 1000 atoms: 0.58 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 1.6 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: 1.26 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: 2.96 Time building geometry restraints manager: 3.86 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: 0.370 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: 2.230 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.340 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- 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 : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.9174 (mtm) cc_final: 0.8761 (mtp) REVERT: A 539 MET cc_start: 0.8834 (mmt) cc_final: 0.8436 (mmm) REVERT: A 718 MET cc_start: 0.8589 (ptt) cc_final: 0.8231 (ptp) REVERT: A 792 LEU cc_start: 0.8963 (mt) cc_final: 0.8653 (tt) REVERT: A 833 ASP cc_start: 0.8146 (t0) cc_final: 0.7568 (t70) REVERT: A 849 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7751 (mt-10) REVERT: A 1047 LEU cc_start: 0.8667 (tp) cc_final: 0.8324 (tp) REVERT: A 1192 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: A 1205 TYR cc_start: 0.7453 (t80) cc_final: 0.7238 (t80) REVERT: A 1259 ASN cc_start: 0.8189 (t0) cc_final: 0.7980 (t0) REVERT: A 1470 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6468 (mt-10) REVERT: A 1502 ARG cc_start: 0.7294 (mtm110) cc_final: 0.6704 (ttp80) outliers start: 9 outliers final: 2 residues processed: 238 average time/residue: 0.2380 time to fit residues: 75.6380 Evaluate side-chains 113 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 1192 GLN Chi-restraints excluded: chain A residue 1379 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.6980 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: 7.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN A 437 GLN A 841 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9185 Z= 0.245 Angle : 0.582 9.874 12490 Z= 0.292 Chirality : 0.041 0.165 1494 Planarity : 0.004 0.040 1527 Dihedral : 8.397 136.427 1343 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.98 % Allowed : 11.78 % Favored : 86.24 % 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: 2.59 (0.25), residues: 1133 helix: 2.45 (0.18), residues: 752 sheet: 0.42 (0.63), residues: 65 loop : 0.25 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 980 HIS 0.004 0.001 HIS A 278 PHE 0.013 0.002 PHE A 293 TYR 0.014 0.001 TYR A1009 ARG 0.004 0.001 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 140 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 422 MET cc_start: 0.8081 (ttp) cc_final: 0.7850 (ttm) REVERT: A 440 MET cc_start: 0.8595 (mmm) cc_final: 0.8224 (mtm) REVERT: A 748 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8649 (m) REVERT: A 1192 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: A 1502 ARG cc_start: 0.7103 (mtm110) cc_final: 0.6768 (ttp80) outliers start: 19 outliers final: 12 residues processed: 136 average time/residue: 0.2052 time to fit residues: 39.5603 Evaluate side-chains 99 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1192 GLN Chi-restraints excluded: chain A residue 1254 ILE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1430 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS ** A1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 ASN A1311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9185 Z= 0.178 Angle : 0.511 8.164 12490 Z= 0.256 Chirality : 0.039 0.192 1494 Planarity : 0.003 0.049 1527 Dihedral : 8.199 138.999 1343 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.71 % Allowed : 12.93 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.90 (0.25), residues: 1133 helix: 2.67 (0.19), residues: 763 sheet: 0.89 (0.60), residues: 75 loop : 0.19 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 980 HIS 0.004 0.001 HIS A1066 PHE 0.013 0.001 PHE A 356 TYR 0.009 0.001 TYR A1523 ARG 0.003 0.000 ARG A1517 *********************** 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 134 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 278 HIS cc_start: 0.5786 (m170) cc_final: 0.5561 (m170) REVERT: A 412 ASN cc_start: 0.8520 (t0) cc_final: 0.8309 (t0) REVERT: A 422 MET cc_start: 0.8055 (ttp) cc_final: 0.7817 (ttm) REVERT: A 440 MET cc_start: 0.8573 (mmm) cc_final: 0.8252 (mtm) REVERT: A 539 MET cc_start: 0.8863 (mmt) cc_final: 0.8266 (mmt) REVERT: A 552 PHE cc_start: 0.8106 (m-80) cc_final: 0.7776 (m-10) REVERT: A 698 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8468 (mtp) REVERT: A 1055 TRP cc_start: 0.8786 (t-100) cc_final: 0.8518 (t-100) REVERT: A 1192 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: A 1194 MET cc_start: 0.9000 (tmm) cc_final: 0.8579 (tmm) REVERT: A 1281 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7455 (t80) REVERT: A 1502 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6759 (ttp80) outliers start: 26 outliers final: 15 residues processed: 124 average time/residue: 0.1828 time to fit residues: 33.3494 Evaluate side-chains 110 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1192 GLN Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1430 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 0.0570 overall best weight: 0.7102 ------------------------------------------------------------------------------- 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: 0.8373 moved from start: 0.3682 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= 0.167 Angle : 0.507 10.380 12490 Z= 0.248 Chirality : 0.039 0.193 1494 Planarity : 0.003 0.050 1527 Dihedral : 7.718 141.478 1340 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.82 % Allowed : 13.87 % Favored : 83.32 % 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: 2.68 (0.19), residues: 764 sheet: 1.02 (0.59), residues: 75 loop : 0.24 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 980 HIS 0.003 0.001 HIS A1065 PHE 0.010 0.001 PHE A 569 TYR 0.011 0.001 TYR A1205 ARG 0.003 0.000 ARG A 381 *********************** 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 135 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 422 MET cc_start: 0.8029 (ttp) cc_final: 0.7795 (ttm) REVERT: A 539 MET cc_start: 0.8812 (mmt) cc_final: 0.8363 (mmt) REVERT: A 698 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8458 (mtp) REVERT: A 1192 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: A 1194 MET cc_start: 0.9081 (tmm) cc_final: 0.8602 (tmm) REVERT: A 1216 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: A 1281 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7426 (t80) REVERT: A 1502 ARG cc_start: 0.7104 (mtm110) cc_final: 0.6676 (ttp80) REVERT: A 1545 MET cc_start: 0.6812 (ppp) cc_final: 0.6486 (ttt) outliers start: 27 outliers final: 17 residues processed: 125 average time/residue: 0.1833 time to fit residues: 33.7437 Evaluate side-chains 109 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1192 GLN Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1430 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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: 0.8418 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9185 Z= 0.214 Angle : 0.512 8.016 12490 Z= 0.254 Chirality : 0.040 0.195 1494 Planarity : 0.003 0.052 1527 Dihedral : 7.652 148.364 1340 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.82 % Allowed : 15.22 % Favored : 81.96 % 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: 2.91 (0.25), residues: 1133 helix: 2.64 (0.19), residues: 764 sheet: 1.19 (0.59), residues: 75 loop : 0.21 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1260 HIS 0.003 0.001 HIS A1065 PHE 0.013 0.001 PHE A 552 TYR 0.015 0.001 TYR A1009 ARG 0.005 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 122 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 422 MET cc_start: 0.8109 (ttp) cc_final: 0.7885 (ttm) REVERT: A 1192 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: A 1194 MET cc_start: 0.9192 (tmm) cc_final: 0.8716 (tmm) REVERT: A 1215 LEU cc_start: 0.8644 (tp) cc_final: 0.8414 (tt) REVERT: A 1216 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: A 1248 LEU cc_start: 0.8414 (mm) cc_final: 0.8152 (mm) REVERT: A 1281 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7393 (t80) REVERT: A 1502 ARG cc_start: 0.7139 (mtm110) cc_final: 0.6825 (ttp80) REVERT: A 1545 MET cc_start: 0.6713 (ppp) cc_final: 0.6447 (ttt) outliers start: 27 outliers final: 19 residues processed: 114 average time/residue: 0.1857 time to fit residues: 31.0544 Evaluate side-chains 108 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1192 GLN Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8409 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9185 Z= 0.191 Angle : 0.513 9.964 12490 Z= 0.251 Chirality : 0.039 0.196 1494 Planarity : 0.004 0.070 1527 Dihedral : 7.579 149.357 1340 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.71 % Allowed : 16.79 % Favored : 80.50 % 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: 2.92 (0.25), residues: 1133 helix: 2.64 (0.19), residues: 764 sheet: 1.43 (0.60), residues: 75 loop : 0.17 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 286 HIS 0.003 0.001 HIS A1001 PHE 0.011 0.001 PHE A 552 TYR 0.011 0.001 TYR A1523 ARG 0.009 0.000 ARG A1542 *********************** 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 123 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 422 MET cc_start: 0.8087 (ttp) cc_final: 0.7823 (ttm) REVERT: A 590 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8263 (ttp80) REVERT: A 1071 LYS cc_start: 0.8967 (tptt) cc_final: 0.8744 (tptm) REVERT: A 1192 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: A 1194 MET cc_start: 0.9165 (tmm) cc_final: 0.8668 (tmm) REVERT: A 1216 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: A 1248 LEU cc_start: 0.8458 (mm) cc_final: 0.8171 (mm) REVERT: A 1281 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7401 (t80) REVERT: A 1502 ARG cc_start: 0.7149 (mtm110) cc_final: 0.6667 (ttp80) REVERT: A 1545 MET cc_start: 0.6817 (ppp) cc_final: 0.6534 (ttt) outliers start: 26 outliers final: 20 residues processed: 117 average time/residue: 0.1975 time to fit residues: 33.3744 Evaluate side-chains 110 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1192 GLN Chi-restraints excluded: chain A residue 1205 TYR Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1430 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8408 moved from start: 0.4225 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= 0.186 Angle : 0.508 10.807 12490 Z= 0.250 Chirality : 0.040 0.209 1494 Planarity : 0.003 0.053 1527 Dihedral : 7.512 148.566 1340 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.71 % Allowed : 16.48 % Favored : 80.81 % 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: 2.91 (0.25), residues: 1133 helix: 2.62 (0.19), residues: 764 sheet: 1.56 (0.61), residues: 75 loop : 0.17 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 423 HIS 0.003 0.001 HIS A1001 PHE 0.012 0.001 PHE A1149 TYR 0.011 0.001 TYR A1523 ARG 0.008 0.000 ARG A1542 *********************** 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 118 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 422 MET cc_start: 0.8044 (ttp) cc_final: 0.7771 (ttm) REVERT: A 549 LEU cc_start: 0.8860 (tt) cc_final: 0.8653 (tt) REVERT: A 590 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.8257 (ttp80) REVERT: A 1071 LYS cc_start: 0.8976 (tptt) cc_final: 0.8754 (tptm) REVERT: A 1192 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: A 1194 MET cc_start: 0.9179 (tmm) cc_final: 0.8668 (tmm) REVERT: A 1216 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: A 1248 LEU cc_start: 0.8406 (mm) cc_final: 0.8102 (mm) REVERT: A 1281 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7398 (t80) REVERT: A 1502 ARG cc_start: 0.7141 (mtm110) cc_final: 0.6667 (ttp80) outliers start: 26 outliers final: 22 residues processed: 111 average time/residue: 0.2062 time to fit residues: 33.4407 Evaluate side-chains 110 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1192 GLN Chi-restraints excluded: chain A residue 1205 TYR Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9185 Z= 0.236 Angle : 0.535 11.019 12490 Z= 0.263 Chirality : 0.040 0.226 1494 Planarity : 0.003 0.052 1527 Dihedral : 7.581 149.545 1340 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.92 % Allowed : 16.58 % Favored : 80.50 % 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: 2.79 (0.25), residues: 1133 helix: 2.51 (0.19), residues: 765 sheet: 1.57 (0.61), residues: 75 loop : 0.16 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1260 HIS 0.003 0.001 HIS A1065 PHE 0.013 0.001 PHE A1149 TYR 0.017 0.001 TYR A1009 ARG 0.006 0.000 ARG A1542 *********************** 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 116 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.8900 (tt) cc_final: 0.8685 (tt) REVERT: A 590 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8272 (ttp80) REVERT: A 1071 LYS cc_start: 0.8991 (tptt) cc_final: 0.8764 (tptm) REVERT: A 1192 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8101 (mp10) REVERT: A 1194 MET cc_start: 0.9208 (tmm) cc_final: 0.8685 (tmm) REVERT: A 1215 LEU cc_start: 0.8616 (tp) cc_final: 0.8313 (tt) REVERT: A 1216 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: A 1248 LEU cc_start: 0.8430 (mm) cc_final: 0.8088 (mm) REVERT: A 1281 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7385 (t80) REVERT: A 1502 ARG cc_start: 0.7192 (mtm110) cc_final: 0.6788 (ttp-110) outliers start: 28 outliers final: 21 residues processed: 109 average time/residue: 0.2008 time to fit residues: 31.5424 Evaluate side-chains 108 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1192 GLN Chi-restraints excluded: chain A residue 1205 TYR Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1090 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9185 Z= 0.179 Angle : 0.502 6.991 12490 Z= 0.247 Chirality : 0.039 0.213 1494 Planarity : 0.003 0.052 1527 Dihedral : 7.437 145.042 1340 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.92 % Allowed : 16.79 % Favored : 80.29 % 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: 2.64 (0.19), residues: 764 sheet: 1.67 (0.62), residues: 74 loop : 0.17 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 423 HIS 0.003 0.001 HIS A1065 PHE 0.012 0.001 PHE A1149 TYR 0.010 0.001 TYR A1523 ARG 0.005 0.000 ARG A1542 *********************** 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 116 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 539 MET cc_start: 0.8904 (mmt) cc_final: 0.8485 (mmt) REVERT: A 549 LEU cc_start: 0.8875 (tt) cc_final: 0.8640 (tt) REVERT: A 590 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8254 (ttp80) REVERT: A 1071 LYS cc_start: 0.9009 (tptt) cc_final: 0.8794 (tptm) REVERT: A 1192 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: A 1194 MET cc_start: 0.9174 (tmm) cc_final: 0.8658 (tmm) REVERT: A 1215 LEU cc_start: 0.8578 (tp) cc_final: 0.8268 (tt) REVERT: A 1216 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: A 1248 LEU cc_start: 0.8354 (mm) cc_final: 0.8035 (mm) REVERT: A 1281 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7365 (t80) REVERT: A 1502 ARG cc_start: 0.7165 (mtm110) cc_final: 0.6861 (ttp-110) outliers start: 28 outliers final: 20 residues processed: 108 average time/residue: 0.1857 time to fit residues: 29.5320 Evaluate side-chains 103 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1192 GLN Chi-restraints excluded: chain A residue 1205 TYR Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1514 VAL 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: 1.9990 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN A1090 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9185 Z= 0.209 Angle : 0.529 12.010 12490 Z= 0.258 Chirality : 0.040 0.205 1494 Planarity : 0.003 0.052 1527 Dihedral : 7.337 138.109 1340 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.82 % Allowed : 17.10 % 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: 2.93 (0.25), residues: 1133 helix: 2.63 (0.18), residues: 764 sheet: 1.61 (0.62), residues: 74 loop : 0.18 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 423 HIS 0.003 0.001 HIS A1065 PHE 0.012 0.001 PHE A1149 TYR 0.012 0.001 TYR A1523 ARG 0.004 0.000 ARG A1542 ********************** 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 110 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 549 LEU cc_start: 0.8865 (tt) cc_final: 0.8640 (tt) REVERT: A 590 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8257 (ttp80) REVERT: A 1056 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8161 (ptp) REVERT: A 1071 LYS cc_start: 0.9017 (tptt) cc_final: 0.8804 (tptm) REVERT: A 1192 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: A 1194 MET cc_start: 0.9192 (tmm) cc_final: 0.8664 (tmm) REVERT: A 1215 LEU cc_start: 0.8586 (tp) cc_final: 0.8286 (tt) REVERT: A 1216 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: A 1248 LEU cc_start: 0.8385 (mm) cc_final: 0.8043 (mm) REVERT: A 1281 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7378 (t80) REVERT: A 1502 ARG cc_start: 0.7160 (mtm110) cc_final: 0.6865 (ttp-110) outliers start: 27 outliers final: 21 residues processed: 103 average time/residue: 0.1999 time to fit residues: 29.9105 Evaluate side-chains 106 residues out of total 986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1162 SER Chi-restraints excluded: chain A residue 1192 GLN Chi-restraints excluded: chain A residue 1205 TYR Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1332 ILE Chi-restraints excluded: chain A residue 1379 HIS Chi-restraints excluded: chain A residue 1398 SER Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1474 SER Chi-restraints excluded: chain A residue 1514 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN A1090 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093601 restraints weight = 14561.819| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.48 r_work: 0.2999 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9185 Z= 0.174 Angle : 0.500 7.874 12490 Z= 0.245 Chirality : 0.039 0.199 1494 Planarity : 0.003 0.052 1527 Dihedral : 7.162 129.349 1340 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.71 % Allowed : 16.79 % Favored : 80.50 % 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: 2.70 (0.18), residues: 764 sheet: 1.69 (0.62), residues: 74 loop : 0.19 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 286 HIS 0.003 0.001 HIS A1065 PHE 0.011 0.001 PHE A1149 TYR 0.010 0.001 TYR A1523 ARG 0.004 0.000 ARG A1542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1810.92 seconds wall clock time: 33 minutes 21.80 seconds (2001.80 seconds total)