Starting phenix.real_space_refine on Thu Sep 26 04:06:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/09_2024/7elc_31180.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/09_2024/7elc_31180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/09_2024/7elc_31180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/09_2024/7elc_31180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/09_2024/7elc_31180.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elc_31180/09_2024/7elc_31180.cif" } resolution = 3.1 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 4 6.06 5 P 7 5.49 5 S 83 5.16 5 C 7458 2.51 5 N 2002 2.21 5 O 2199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11754 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11193 Classifications: {'peptide': 1409} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 39, 'TRANS': 1369} Chain breaks: 15 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2014 SG CYS A 284 50.115 66.499 25.945 1.00 39.04 S ATOM 2038 SG CYS A 287 53.363 66.957 23.538 1.00 38.92 S ATOM 3378 SG CYS A 470 49.797 68.522 22.607 1.00 67.43 S ATOM 9952 SG CYS A1650 39.911 15.154 42.832 1.00 76.77 S ATOM 9965 SG CYS A1652 36.471 15.298 43.227 1.00 78.38 S ATOM 9984 SG CYS A1655 39.918 18.510 43.735 1.00 66.72 S ATOM 10056 SG CYS A1664 38.079 16.333 45.513 1.00 59.44 S ATOM 11254 SG CYS B 39 23.348 77.702 52.665 1.00 45.38 S ATOM 11275 SG CYS B 42 25.973 79.094 51.654 1.00 44.44 S ATOM 11409 SG CYS B 58 21.496 79.659 50.588 1.00 59.01 S ATOM 11434 SG CYS B 61 23.404 77.092 49.258 1.00 58.68 S ATOM 11357 SG CYS B 52 16.244 70.508 55.345 1.00 68.57 S ATOM 11524 SG CYS B 72 18.943 69.558 53.533 1.00 53.78 S ATOM 11548 SG CYS B 75 18.152 67.872 56.362 1.00 52.91 S Time building chain proxies: 7.16, per 1000 atoms: 0.61 Number of scatterers: 11754 At special positions: 0 Unit cell: (119, 110, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Mn 1 24.99 S 83 16.00 P 7 15.00 O 2199 8.00 N 2002 7.00 C 7458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1650 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1655 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1652 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1664 " pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 39 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 52 " Number of angles added : 18 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 52.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 4.014A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 57 removed outlier: 3.751A pdb=" N ALA A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 removed outlier: 3.763A pdb=" N ASN A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 133 removed outlier: 3.930A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 removed outlier: 3.860A pdb=" N ARG A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.536A pdb=" N SER A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.750A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.688A pdb=" N ASP A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.550A pdb=" N LYS A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.872A pdb=" N ASN A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 501 removed outlier: 3.525A pdb=" N GLN A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 579 through 583 removed outlier: 4.392A pdb=" N PHE A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 599 removed outlier: 3.777A pdb=" N LEU A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 623 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.519A pdb=" N ASN A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.722A pdb=" N VAL A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 removed outlier: 3.894A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'A' and resid 712 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1197 through 1208 removed outlier: 4.227A pdb=" N MET A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1239 through 1248 Processing helix chain 'A' and resid 1264 through 1275 removed outlier: 4.381A pdb=" N GLN A1275 " --> pdb=" O HIS A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 3.522A pdb=" N ASN A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1450 removed outlier: 3.580A pdb=" N THR A1437 " --> pdb=" O THR A1433 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1468 Processing helix chain 'A' and resid 1472 through 1485 Processing helix chain 'A' and resid 1489 through 1507 Processing helix chain 'A' and resid 1514 through 1520 Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1537 through 1545 Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 4.247A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1625 Processing helix chain 'A' and resid 1639 through 1645 Processing helix chain 'A' and resid 1665 through 1669 removed outlier: 3.522A pdb=" N LEU A1668 " --> pdb=" O ASN A1665 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A1669 " --> pdb=" O ASN A1666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1665 through 1669' Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.575A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1698 Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1744 through 1750 Processing helix chain 'A' and resid 1774 through 1783 removed outlier: 3.549A pdb=" N ALA A1778 " --> pdb=" O ASP A1774 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A1780 " --> pdb=" O CYS A1776 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A1783 " --> pdb=" O LEU A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1793 Processing helix chain 'A' and resid 1805 through 1809 Processing helix chain 'B' and resid 58 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 93 removed outlier: 7.011A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 105 removed outlier: 6.290A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.633A pdb=" N CYS A 528 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG A 553 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR A 572 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR A 555 " --> pdb=" O SER A 570 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER A 570 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 557 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 735 through 736 removed outlier: 6.941A pdb=" N PHE A1117 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1379 through 1381 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA8, first strand: chain 'A' and resid 1716 through 1719 Processing sheet with id=AA9, first strand: chain 'B' and resid 50 through 51 553 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3765 1.34 - 1.46: 2121 1.46 - 1.58: 5955 1.58 - 1.70: 13 1.70 - 1.82: 116 Bond restraints: 11970 Sorted by residual: bond pdb=" CA ASP A1470 " pdb=" CB ASP A1470 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 8.09e-01 bond pdb=" CB ASP A1470 " pdb=" CG ASP A1470 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.68e-01 bond pdb=" CA ILE A 381 " pdb=" CB ILE A 381 " ideal model delta sigma weight residual 1.550 1.542 0.009 1.03e-02 9.43e+03 7.20e-01 bond pdb=" C ARG A 691 " pdb=" O ARG A 691 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.17e-02 7.31e+03 7.18e-01 bond pdb=" CB VAL A 358 " pdb=" CG1 VAL A 358 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.23e-01 ... (remaining 11965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 15945 1.89 - 3.77: 191 3.77 - 5.66: 24 5.66 - 7.54: 5 7.54 - 9.43: 1 Bond angle restraints: 16166 Sorted by residual: angle pdb=" N GLU A 427 " pdb=" CA GLU A 427 " pdb=" C GLU A 427 " ideal model delta sigma weight residual 114.56 109.02 5.54 1.27e+00 6.20e-01 1.90e+01 angle pdb=" C CYS B 42 " pdb=" N TRP B 43 " pdb=" CA TRP B 43 " ideal model delta sigma weight residual 121.54 127.18 -5.64 1.91e+00 2.74e-01 8.73e+00 angle pdb=" CA TRP B 43 " pdb=" CB TRP B 43 " pdb=" CG TRP B 43 " ideal model delta sigma weight residual 113.60 118.98 -5.38 1.90e+00 2.77e-01 8.02e+00 angle pdb=" CA GLU A 427 " pdb=" C GLU A 427 " pdb=" N ILE A 428 " ideal model delta sigma weight residual 119.26 116.16 3.10 1.14e+00 7.69e-01 7.40e+00 angle pdb=" CA LEU A 435 " pdb=" CB LEU A 435 " pdb=" CG LEU A 435 " ideal model delta sigma weight residual 116.30 125.73 -9.43 3.50e+00 8.16e-02 7.26e+00 ... (remaining 16161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6539 17.97 - 35.94: 559 35.94 - 53.91: 139 53.91 - 71.87: 35 71.87 - 89.84: 12 Dihedral angle restraints: 7284 sinusoidal: 3032 harmonic: 4252 Sorted by residual: dihedral pdb=" CB CYS A 55 " pdb=" SG CYS A 55 " pdb=" SG CYS A 60 " pdb=" CB CYS A 60 " ideal model delta sinusoidal sigma weight residual -86.00 -39.30 -46.70 1 1.00e+01 1.00e-02 3.02e+01 dihedral pdb=" CA SER A1432 " pdb=" C SER A1432 " pdb=" N THR A1433 " pdb=" CA THR A1433 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LYS A1364 " pdb=" C LYS A1364 " pdb=" N LEU A1365 " pdb=" CA LEU A1365 " ideal model delta harmonic sigma weight residual 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 7281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1183 0.031 - 0.062: 468 0.062 - 0.092: 135 0.092 - 0.123: 66 0.123 - 0.154: 6 Chirality restraints: 1858 Sorted by residual: chirality pdb=" CB ILE A1510 " pdb=" CA ILE A1510 " pdb=" CG1 ILE A1510 " pdb=" CG2 ILE A1510 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CB ILE A 87 " pdb=" CA ILE A 87 " pdb=" CG1 ILE A 87 " pdb=" CG2 ILE A 87 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA ASP A1470 " pdb=" N ASP A1470 " pdb=" C ASP A1470 " pdb=" CB ASP A1470 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1855 not shown) Planarity restraints: 2014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1280 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A1281 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A1281 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1281 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1753 " -0.021 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A1754 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A1754 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1754 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 710 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 711 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 711 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 711 " 0.017 5.00e-02 4.00e+02 ... (remaining 2011 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 969 2.74 - 3.28: 12104 3.28 - 3.82: 19734 3.82 - 4.36: 24062 4.36 - 4.90: 40471 Nonbonded interactions: 97340 Sorted by model distance: nonbonded pdb=" OD1 ASP A 769 " pdb=" OG1 THR A 772 " model vdw 2.198 3.040 nonbonded pdb=" OG SER A 538 " pdb=" OD1 ASN A 562 " model vdw 2.235 3.040 nonbonded pdb=" O ASP A 370 " pdb=" OG SER A 374 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP A1420 " pdb=" NH1 ARG A1476 " model vdw 2.237 3.120 nonbonded pdb=" O LYS A1191 " pdb=" OG1 THR A1195 " model vdw 2.250 3.040 ... (remaining 97335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.580 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.003 0.027 11970 Z= 0.182 Angle : 0.548 9.427 16166 Z= 0.305 Chirality : 0.039 0.154 1858 Planarity : 0.003 0.035 2014 Dihedral : 15.027 89.844 4506 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.27 % Favored : 90.66 % Rotamer: Outliers : 2.73 % Allowed : 9.64 % Favored : 87.63 % 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 (0.20), residues: 1424 helix: -0.84 (0.17), residues: 733 sheet: -2.89 (0.39), residues: 104 loop : -3.40 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1680 HIS 0.003 0.001 HIS A 647 PHE 0.018 0.001 PHE A 533 TYR 0.009 0.001 TYR A 534 ARG 0.002 0.000 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 225 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 232 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7059 (tm-30) REVERT: A 357 MET cc_start: 0.8158 (tpp) cc_final: 0.7516 (mmt) REVERT: A 766 ASP cc_start: 0.7883 (p0) cc_final: 0.7635 (p0) REVERT: A 1143 ARG cc_start: 0.7145 (tmm-80) cc_final: 0.6681 (tpp80) REVERT: A 1272 GLN cc_start: 0.7779 (mt0) cc_final: 0.7479 (mt0) REVERT: A 1391 GLU cc_start: 0.7493 (pt0) cc_final: 0.7147 (pm20) REVERT: A 1414 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 1527 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8136 (tp) REVERT: A 1625 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7547 (mmp) REVERT: B 65 MET cc_start: 0.8039 (mtm) cc_final: 0.7761 (mtm) REVERT: B 68 ASN cc_start: 0.6534 (OUTLIER) cc_final: 0.6129 (p0) outliers start: 36 outliers final: 23 residues processed: 250 average time/residue: 0.2828 time to fit residues: 97.0674 Evaluate side-chains 199 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 0.0670 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 125 ASN A 148 ASN A 185 GLN A 189 HIS A 359 ASN A 442 ASN A 522 ASN A 546 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 ASN A1206 GLN A1231 HIS A1275 GLN A1283 HIS A1296 HIS A1331 GLN A1463 GLN A1496 ASN A1551 ASN A1712 ASN A1726 GLN A1743 ASN A1783 ASN A1791 HIS ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11970 Z= 0.187 Angle : 0.562 9.901 16166 Z= 0.283 Chirality : 0.041 0.170 1858 Planarity : 0.004 0.040 2014 Dihedral : 9.937 74.196 1720 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.62 % Favored : 90.31 % Rotamer: Outliers : 3.41 % Allowed : 12.59 % Favored : 83.99 % 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: -1.96 (0.22), residues: 1424 helix: 0.10 (0.18), residues: 750 sheet: -2.53 (0.46), residues: 94 loop : -3.03 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1192 HIS 0.003 0.001 HIS A 647 PHE 0.021 0.001 PHE A1511 TYR 0.010 0.001 TYR A 572 ARG 0.005 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 192 time to evaluate : 1.465 Fit side-chains REVERT: A 357 MET cc_start: 0.8208 (tpp) cc_final: 0.7624 (mmt) REVERT: A 381 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6490 (tt) REVERT: A 736 VAL cc_start: 0.8255 (t) cc_final: 0.8044 (t) REVERT: A 1143 ARG cc_start: 0.7159 (tmm-80) cc_final: 0.6665 (tpp80) REVERT: A 1391 GLU cc_start: 0.7285 (pt0) cc_final: 0.6769 (pm20) REVERT: A 1462 ASP cc_start: 0.6489 (t0) cc_final: 0.6275 (t0) REVERT: A 1527 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7982 (tp) REVERT: B 36 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7224 (ptt-90) REVERT: B 70 GLU cc_start: 0.7294 (tp30) cc_final: 0.6513 (tp30) outliers start: 45 outliers final: 30 residues processed: 227 average time/residue: 0.2419 time to fit residues: 78.7903 Evaluate side-chains 201 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 335 ASN A 359 ASN A 476 GLN A 628 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN A1734 ASN A1812 HIS ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11970 Z= 0.222 Angle : 0.577 11.938 16166 Z= 0.288 Chirality : 0.041 0.147 1858 Planarity : 0.004 0.042 2014 Dihedral : 9.640 73.429 1713 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.69 % Favored : 90.24 % Rotamer: Outliers : 3.87 % Allowed : 15.63 % 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: -1.58 (0.22), residues: 1424 helix: 0.44 (0.19), residues: 751 sheet: -2.32 (0.49), residues: 92 loop : -2.91 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1549 HIS 0.006 0.001 HIS A 189 PHE 0.021 0.001 PHE A1105 TYR 0.008 0.001 TYR A1318 ARG 0.005 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 183 time to evaluate : 1.383 Fit side-chains REVERT: A 166 GLU cc_start: 0.4334 (OUTLIER) cc_final: 0.4054 (mp0) REVERT: A 357 MET cc_start: 0.8232 (tpp) cc_final: 0.7661 (mmt) REVERT: A 381 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6518 (tt) REVERT: A 1143 ARG cc_start: 0.7272 (tmm-80) cc_final: 0.6651 (tpp80) REVERT: A 1268 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6206 (tp30) REVERT: A 1307 GLU cc_start: 0.7509 (tp30) cc_final: 0.7302 (tp30) REVERT: A 1391 GLU cc_start: 0.7332 (pt0) cc_final: 0.6944 (pm20) REVERT: A 1462 ASP cc_start: 0.6531 (t0) cc_final: 0.6295 (t0) REVERT: A 1527 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7974 (tp) REVERT: B 36 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7330 (ptt-90) REVERT: B 68 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.6266 (p0) REVERT: B 70 GLU cc_start: 0.7312 (tp30) cc_final: 0.6531 (tp30) outliers start: 51 outliers final: 36 residues processed: 221 average time/residue: 0.2444 time to fit residues: 77.1773 Evaluate side-chains 213 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 0.0770 chunk 131 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11970 Z= 0.208 Angle : 0.572 12.485 16166 Z= 0.284 Chirality : 0.041 0.149 1858 Planarity : 0.004 0.043 2014 Dihedral : 9.571 73.450 1712 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.27 % Favored : 90.66 % Rotamer: Outliers : 4.17 % Allowed : 16.39 % Favored : 79.44 % 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: -1.32 (0.22), residues: 1424 helix: 0.67 (0.19), residues: 751 sheet: -2.22 (0.50), residues: 92 loop : -2.81 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 43 HIS 0.008 0.001 HIS A 189 PHE 0.023 0.001 PHE A1105 TYR 0.008 0.001 TYR A 695 ARG 0.006 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 188 time to evaluate : 1.306 Fit side-chains REVERT: A 166 GLU cc_start: 0.4250 (OUTLIER) cc_final: 0.3946 (mp0) REVERT: A 357 MET cc_start: 0.8247 (tpp) cc_final: 0.7658 (mmt) REVERT: A 381 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6656 (tt) REVERT: A 1143 ARG cc_start: 0.7291 (tmm-80) cc_final: 0.6676 (tpp80) REVERT: A 1268 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6215 (tp30) REVERT: A 1307 GLU cc_start: 0.7366 (tp30) cc_final: 0.7162 (tp30) REVERT: A 1391 GLU cc_start: 0.7169 (pt0) cc_final: 0.6863 (pm20) REVERT: A 1527 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8053 (tm) REVERT: B 36 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7301 (ptt-90) REVERT: B 68 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.6268 (p0) REVERT: B 70 GLU cc_start: 0.7323 (tp30) cc_final: 0.6481 (tp30) outliers start: 55 outliers final: 39 residues processed: 229 average time/residue: 0.2310 time to fit residues: 76.2456 Evaluate side-chains 214 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 169 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1625 MET Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 359 ASN A 425 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11970 Z= 0.211 Angle : 0.576 12.829 16166 Z= 0.289 Chirality : 0.041 0.264 1858 Planarity : 0.004 0.043 2014 Dihedral : 9.600 74.062 1712 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.62 % Favored : 90.31 % Rotamer: Outliers : 4.32 % Allowed : 17.68 % Favored : 78.00 % 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: -1.14 (0.23), residues: 1424 helix: 0.78 (0.19), residues: 759 sheet: -2.13 (0.50), residues: 92 loop : -2.74 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 43 HIS 0.003 0.001 HIS A 647 PHE 0.025 0.001 PHE A1105 TYR 0.014 0.001 TYR A 534 ARG 0.006 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 182 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.4346 (OUTLIER) cc_final: 0.4013 (mp0) REVERT: A 357 MET cc_start: 0.8237 (tpp) cc_final: 0.7664 (mmt) REVERT: A 381 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6707 (tt) REVERT: A 595 MET cc_start: 0.8758 (mmm) cc_final: 0.8267 (mtt) REVERT: A 1143 ARG cc_start: 0.7240 (tmm-80) cc_final: 0.6619 (tpp80) REVERT: A 1268 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.5911 (mm-30) REVERT: A 1272 GLN cc_start: 0.7735 (mt0) cc_final: 0.6993 (mm-40) REVERT: A 1391 GLU cc_start: 0.7131 (pt0) cc_final: 0.6752 (pm20) REVERT: A 1527 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8080 (tm) REVERT: A 1657 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8022 (pt) REVERT: B 36 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7328 (ptt-90) REVERT: B 68 ASN cc_start: 0.6785 (OUTLIER) cc_final: 0.6318 (p0) REVERT: B 70 GLU cc_start: 0.7350 (tp30) cc_final: 0.6522 (tp30) outliers start: 57 outliers final: 39 residues processed: 225 average time/residue: 0.2325 time to fit residues: 75.8188 Evaluate side-chains 217 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 425 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11970 Z= 0.211 Angle : 0.575 12.942 16166 Z= 0.289 Chirality : 0.041 0.192 1858 Planarity : 0.004 0.043 2014 Dihedral : 9.512 74.480 1709 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.41 % Favored : 90.52 % Rotamer: Outliers : 4.63 % Allowed : 17.91 % Favored : 77.47 % 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: -1.01 (0.23), residues: 1424 helix: 0.87 (0.19), residues: 763 sheet: -2.03 (0.51), residues: 92 loop : -2.68 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 43 HIS 0.003 0.001 HIS A 647 PHE 0.023 0.001 PHE A1105 TYR 0.008 0.001 TYR A 695 ARG 0.005 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 175 time to evaluate : 1.716 Fit side-chains REVERT: A 166 GLU cc_start: 0.4370 (OUTLIER) cc_final: 0.4020 (mp0) REVERT: A 357 MET cc_start: 0.8275 (tpp) cc_final: 0.7690 (mmt) REVERT: A 381 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6672 (tt) REVERT: A 595 MET cc_start: 0.8754 (mmm) cc_final: 0.8297 (mtt) REVERT: A 743 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7463 (mtmm) REVERT: A 1143 ARG cc_start: 0.7235 (tmm-80) cc_final: 0.6612 (tpp80) REVERT: A 1268 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5918 (mm-30) REVERT: A 1272 GLN cc_start: 0.7736 (mt0) cc_final: 0.6980 (mm-40) REVERT: A 1391 GLU cc_start: 0.7066 (pt0) cc_final: 0.6746 (pm20) REVERT: A 1527 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7983 (tm) REVERT: A 1654 ILE cc_start: 0.7723 (mp) cc_final: 0.7312 (mt) REVERT: A 1657 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8000 (pt) REVERT: B 68 ASN cc_start: 0.6939 (OUTLIER) cc_final: 0.6450 (p0) REVERT: B 70 GLU cc_start: 0.7334 (tp30) cc_final: 0.6504 (tp30) outliers start: 61 outliers final: 46 residues processed: 217 average time/residue: 0.2432 time to fit residues: 77.4104 Evaluate side-chains 217 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 164 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 86 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 149 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS A 438 GLN A 629 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN A1297 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 11970 Z= 0.341 Angle : 0.646 13.006 16166 Z= 0.326 Chirality : 0.044 0.190 1858 Planarity : 0.004 0.045 2014 Dihedral : 9.644 77.069 1705 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.04 % Favored : 89.89 % Rotamer: Outliers : 4.55 % Allowed : 19.20 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.23 (0.22), residues: 1424 helix: 0.59 (0.18), residues: 773 sheet: -2.22 (0.47), residues: 99 loop : -2.64 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 43 HIS 0.008 0.001 HIS A 425 PHE 0.030 0.002 PHE A1105 TYR 0.010 0.002 TYR A 214 ARG 0.003 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 170 time to evaluate : 1.307 Fit side-chains REVERT: A 166 GLU cc_start: 0.4555 (OUTLIER) cc_final: 0.4164 (mp0) REVERT: A 357 MET cc_start: 0.8284 (tpp) cc_final: 0.7668 (mmt) REVERT: A 376 ARG cc_start: 0.7839 (mmt-90) cc_final: 0.7074 (mmt-90) REVERT: A 381 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6633 (tt) REVERT: A 384 GLN cc_start: 0.6045 (mm-40) cc_final: 0.5816 (mm-40) REVERT: A 595 MET cc_start: 0.8795 (mmm) cc_final: 0.8426 (mtt) REVERT: A 606 MET cc_start: 0.8510 (ptm) cc_final: 0.8284 (ptt) REVERT: A 743 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7531 (mtmm) REVERT: A 1143 ARG cc_start: 0.7274 (tmm-80) cc_final: 0.6749 (tpp80) REVERT: A 1268 GLU cc_start: 0.6723 (mp0) cc_final: 0.5899 (mm-30) REVERT: A 1462 ASP cc_start: 0.6735 (t0) cc_final: 0.6532 (t0) REVERT: A 1657 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8059 (pt) REVERT: B 68 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6492 (p0) REVERT: B 70 GLU cc_start: 0.7340 (tp30) cc_final: 0.6537 (tp30) outliers start: 60 outliers final: 47 residues processed: 215 average time/residue: 0.2313 time to fit residues: 72.5279 Evaluate side-chains 214 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 162 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1388 VAL Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 359 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11970 Z= 0.247 Angle : 0.593 12.634 16166 Z= 0.299 Chirality : 0.042 0.167 1858 Planarity : 0.004 0.044 2014 Dihedral : 9.567 76.860 1704 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.27 % Favored : 90.66 % Rotamer: Outliers : 4.70 % Allowed : 19.04 % Favored : 76.25 % 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: -1.01 (0.23), residues: 1424 helix: 0.80 (0.19), residues: 764 sheet: -1.93 (0.51), residues: 94 loop : -2.58 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 43 HIS 0.003 0.001 HIS A 647 PHE 0.028 0.002 PHE A1105 TYR 0.017 0.001 TYR A 534 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 175 time to evaluate : 1.129 Fit side-chains REVERT: A 144 ARG cc_start: 0.6019 (mtm-85) cc_final: 0.5492 (mmp-170) REVERT: A 166 GLU cc_start: 0.4551 (OUTLIER) cc_final: 0.4145 (mp0) REVERT: A 357 MET cc_start: 0.8267 (tpp) cc_final: 0.7632 (mmt) REVERT: A 376 ARG cc_start: 0.7737 (mmt-90) cc_final: 0.7080 (mmt-90) REVERT: A 381 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6544 (tt) REVERT: A 595 MET cc_start: 0.8778 (mmm) cc_final: 0.8400 (mtt) REVERT: A 736 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8128 (t) REVERT: A 743 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7452 (mtmm) REVERT: A 1143 ARG cc_start: 0.7266 (tmm-80) cc_final: 0.6722 (tpp80) REVERT: A 1268 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.5910 (mm-30) REVERT: A 1272 GLN cc_start: 0.7642 (mt0) cc_final: 0.6873 (mm-40) REVERT: A 1462 ASP cc_start: 0.6887 (t0) cc_final: 0.6614 (t0) REVERT: A 1654 ILE cc_start: 0.7763 (mp) cc_final: 0.7350 (mt) REVERT: A 1657 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8078 (pt) REVERT: B 68 ASN cc_start: 0.6982 (OUTLIER) cc_final: 0.6503 (p0) REVERT: B 70 GLU cc_start: 0.7339 (tp30) cc_final: 0.7055 (tp30) outliers start: 62 outliers final: 50 residues processed: 219 average time/residue: 0.2226 time to fit residues: 71.6939 Evaluate side-chains 225 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 168 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 5.9990 chunk 121 optimal weight: 0.0980 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 384 GLN A 425 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1666 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11970 Z= 0.209 Angle : 0.596 12.109 16166 Z= 0.298 Chirality : 0.041 0.164 1858 Planarity : 0.004 0.044 2014 Dihedral : 9.484 75.442 1704 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.62 % Favored : 90.31 % Rotamer: Outliers : 4.25 % Allowed : 19.95 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1424 helix: 0.90 (0.19), residues: 765 sheet: -1.98 (0.51), residues: 92 loop : -2.51 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 43 HIS 0.003 0.001 HIS A 647 PHE 0.027 0.001 PHE A1511 TYR 0.009 0.001 TYR A 534 ARG 0.004 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 175 time to evaluate : 1.232 Fit side-chains REVERT: A 144 ARG cc_start: 0.5857 (mtm-85) cc_final: 0.5466 (mmp-170) REVERT: A 166 GLU cc_start: 0.4504 (OUTLIER) cc_final: 0.4133 (mp0) REVERT: A 357 MET cc_start: 0.8264 (tpp) cc_final: 0.7627 (mmt) REVERT: A 376 ARG cc_start: 0.7626 (mmt-90) cc_final: 0.7055 (mmt-90) REVERT: A 381 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6530 (tt) REVERT: A 595 MET cc_start: 0.8764 (mmm) cc_final: 0.8367 (mtt) REVERT: A 713 ARG cc_start: 0.7411 (ttt90) cc_final: 0.7205 (tpt90) REVERT: A 736 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.8002 (t) REVERT: A 743 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7319 (mmtt) REVERT: A 1143 ARG cc_start: 0.7255 (tmm-80) cc_final: 0.6704 (tpp80) REVERT: A 1268 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.5909 (mm-30) REVERT: A 1272 GLN cc_start: 0.7603 (mt0) cc_final: 0.6847 (mm-40) REVERT: A 1654 ILE cc_start: 0.7739 (mp) cc_final: 0.7281 (mt) REVERT: A 1657 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8068 (pt) REVERT: B 68 ASN cc_start: 0.6975 (OUTLIER) cc_final: 0.6549 (p0) REVERT: B 70 GLU cc_start: 0.7346 (tp30) cc_final: 0.7046 (tp30) outliers start: 56 outliers final: 45 residues processed: 216 average time/residue: 0.2405 time to fit residues: 75.7570 Evaluate side-chains 220 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 168 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11970 Z= 0.230 Angle : 0.612 11.839 16166 Z= 0.305 Chirality : 0.042 0.175 1858 Planarity : 0.004 0.045 2014 Dihedral : 9.434 75.730 1700 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.20 % Favored : 90.73 % Rotamer: Outliers : 4.25 % Allowed : 20.11 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.23), residues: 1424 helix: 0.92 (0.19), residues: 762 sheet: -1.88 (0.51), residues: 92 loop : -2.47 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1230 HIS 0.003 0.001 HIS A 647 PHE 0.026 0.002 PHE A1511 TYR 0.008 0.001 TYR A 572 ARG 0.004 0.000 ARG A 551 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 163 time to evaluate : 1.406 Fit side-chains REVERT: A 144 ARG cc_start: 0.5823 (mtm-85) cc_final: 0.5466 (mmp-170) REVERT: A 166 GLU cc_start: 0.4507 (OUTLIER) cc_final: 0.4133 (mp0) REVERT: A 357 MET cc_start: 0.8240 (tpp) cc_final: 0.7668 (mmt) REVERT: A 376 ARG cc_start: 0.7606 (mmt-90) cc_final: 0.7046 (mmt-90) REVERT: A 381 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6504 (tt) REVERT: A 595 MET cc_start: 0.8772 (mmm) cc_final: 0.8391 (mtt) REVERT: A 736 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8009 (t) REVERT: A 743 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7368 (mmtt) REVERT: A 1143 ARG cc_start: 0.7265 (tmm-80) cc_final: 0.6710 (tpp80) REVERT: A 1268 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.5906 (mm-30) REVERT: A 1272 GLN cc_start: 0.7608 (mt0) cc_final: 0.6855 (mm-40) REVERT: A 1545 LEU cc_start: 0.8760 (mt) cc_final: 0.8443 (mt) REVERT: A 1654 ILE cc_start: 0.7721 (mp) cc_final: 0.7255 (mt) REVERT: A 1657 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8065 (pt) REVERT: B 68 ASN cc_start: 0.7024 (OUTLIER) cc_final: 0.6571 (p0) REVERT: B 70 GLU cc_start: 0.7352 (tp30) cc_final: 0.7047 (tp30) outliers start: 56 outliers final: 45 residues processed: 202 average time/residue: 0.2335 time to fit residues: 68.8730 Evaluate side-chains 213 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 425 HIS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 737 ASN Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 743 LYS Chi-restraints excluded: chain A residue 799 LYS Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1290 MET Chi-restraints excluded: chain A residue 1317 LEU Chi-restraints excluded: chain A residue 1323 VAL Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1409 CYS Chi-restraints excluded: chain A residue 1426 CYS Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1460 ILE Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1469 VAL Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1634 LYS Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1693 LEU Chi-restraints excluded: chain A residue 1738 GLN Chi-restraints excluded: chain A residue 1788 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 68 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 384 GLN A 425 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.175433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137795 restraints weight = 13311.007| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.04 r_work: 0.3309 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11970 Z= 0.225 Angle : 0.609 11.381 16166 Z= 0.303 Chirality : 0.042 0.180 1858 Planarity : 0.004 0.045 2014 Dihedral : 9.428 75.971 1699 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.41 % Favored : 90.52 % Rotamer: Outliers : 4.17 % Allowed : 20.33 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1424 helix: 1.04 (0.19), residues: 749 sheet: -2.11 (0.48), residues: 92 loop : -2.42 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1717 HIS 0.005 0.001 HIS A 425 PHE 0.027 0.002 PHE A1511 TYR 0.008 0.001 TYR A 695 ARG 0.004 0.000 ARG A1169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2901.92 seconds wall clock time: 52 minutes 42.24 seconds (3162.24 seconds total)