Starting phenix.real_space_refine on Fri Feb 16 00:21:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1q_23618/02_2024/7m1q_23618_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1q_23618/02_2024/7m1q_23618.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1q_23618/02_2024/7m1q_23618_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1q_23618/02_2024/7m1q_23618_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1q_23618/02_2024/7m1q_23618_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1q_23618/02_2024/7m1q_23618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1q_23618/02_2024/7m1q_23618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1q_23618/02_2024/7m1q_23618_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1q_23618/02_2024/7m1q_23618_updated.pdb" } resolution = 2.92 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 8871 2.51 5 N 2338 2.21 5 O 2506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1785": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13780 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13524 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1911, 13506 Classifications: {'peptide': 1911} Incomplete info: {'truncation_to_alanine': 477} Link IDs: {'PTRANS': 97, 'TRANS': 1813} Chain breaks: 13 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1816 Unresolved non-hydrogen angles: 2320 Unresolved non-hydrogen dihedrals: 1482 Unresolved non-hydrogen chiralities: 157 Planarities with less than four sites: {'GLN:plan1': 27, 'ASP:plan': 42, 'TYR:plan': 16, 'ASN:plan1': 21, 'TRP:plan': 5, 'HIS:plan': 16, 'PHE:plan': 26, 'GLU:plan': 63, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1111 Conformer: "B" Number of residues, atoms: 1911, 13506 Classifications: {'peptide': 1911} Incomplete info: {'truncation_to_alanine': 477} Link IDs: {'PTRANS': 97, 'TRANS': 1813} Chain breaks: 13 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1816 Unresolved non-hydrogen angles: 2320 Unresolved non-hydrogen dihedrals: 1482 Unresolved non-hydrogen chiralities: 157 Planarities with less than four sites: {'GLN:plan1': 27, 'ASP:plan': 42, 'TYR:plan': 16, 'ASN:plan1': 21, 'TRP:plan': 5, 'HIS:plan': 16, 'PHE:plan': 26, 'GLU:plan': 63, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1111 bond proxies already assigned to first conformer: 13786 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 156 Unusual residues: {' MG': 1, 'HZL': 1, 'NAG': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 14.02, per 1000 atoms: 1.02 Number of scatterers: 13780 At special positions: 0 Unit cell: (89.5738, 96.5234, 236.289, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 1 15.00 Mg 1 11.99 O 2506 8.00 N 2338 7.00 C 8871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A1588 " " NAG A2303 " - " ASN A1662 " " NAG A2305 " - " ASN A 444 " " NAG A2306 " - " ASN A1469 " " NAG A2307 " - " ASN A 504 " " NAG B 1 " - " ASN A1529 " " NAG C 1 " - " ASN A 415 " Time building additional restraints: 6.08 Conformation dependent library (CDL) restraints added in 5.1 seconds 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 6 sheets defined 48.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 removed outlier: 3.662A pdb=" N ARG A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 45 removed outlier: 3.536A pdb=" N LEU A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Proline residue: A 32 - end of helix removed outlier: 3.737A pdb=" N LEU A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 66 through 77 removed outlier: 3.900A pdb=" N VAL A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'A' and resid 260 through 263 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.790A pdb=" N ASP A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 384 through 394 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 405 through 442 removed outlier: 4.470A pdb=" N SER A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TRP A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 474 through 477 Processing helix chain 'A' and resid 499 through 518 removed outlier: 4.189A pdb=" N ILE A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 543 Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 602 through 605 No H-bonds generated for 'chain 'A' and resid 602 through 605' Processing helix chain 'A' and resid 608 through 624 Processing helix chain 'A' and resid 646 through 661 removed outlier: 4.512A pdb=" N CYS A 654 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE A 655 " --> pdb=" O ASN A 652 " (cutoff:3.500A) Proline residue: A 656 - end of helix Processing helix chain 'A' and resid 664 through 679 Processing helix chain 'A' and resid 683 through 689 Processing helix chain 'A' and resid 695 through 721 Processing helix chain 'A' and resid 730 through 754 removed outlier: 3.683A pdb=" N THR A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 removed outlier: 4.406A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 773 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 774 " --> pdb=" O PHE A 770 " (cutoff:3.500A) Proline residue: A 775 - end of helix removed outlier: 3.640A pdb=" N ALA A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 796 removed outlier: 3.688A pdb=" N LEU A 796 " --> pdb=" O LYS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 814 Processing helix chain 'A' and resid 837 through 860 Processing helix chain 'A' and resid 969 through 977 Processing helix chain 'A' and resid 1020 through 1030 Processing helix chain 'A' and resid 1035 through 1043 Processing helix chain 'A' and resid 1064 through 1076 removed outlier: 3.806A pdb=" N ALA A1075 " --> pdb=" O SER A1071 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1106 Processing helix chain 'A' and resid 1121 through 1123 No H-bonds generated for 'chain 'A' and resid 1121 through 1123' Processing helix chain 'A' and resid 1144 through 1148 Processing helix chain 'A' and resid 1205 through 1215 removed outlier: 3.517A pdb=" N ASP A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1254 Processing helix chain 'A' and resid 1269 through 1276 removed outlier: 4.319A pdb=" N VAL A1276 " --> pdb=" O ILE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1368 removed outlier: 3.671A pdb=" N VAL A1351 " --> pdb=" O THR A1348 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A1352 " --> pdb=" O GLN A1349 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG A1368 " --> pdb=" O HIS A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1374 No H-bonds generated for 'chain 'A' and resid 1371 through 1374' Processing helix chain 'A' and resid 1379 through 1393 Processing helix chain 'A' and resid 1407 through 1409 No H-bonds generated for 'chain 'A' and resid 1407 through 1409' Processing helix chain 'A' and resid 1425 through 1435 Processing helix chain 'A' and resid 1468 through 1476 Processing helix chain 'A' and resid 1530 through 1545 Proline residue: A1539 - end of helix removed outlier: 3.948A pdb=" N SER A1544 " --> pdb=" O ALA A1540 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A1545 " --> pdb=" O LEU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1574 through 1586 Processing helix chain 'A' and resid 1593 through 1609 removed outlier: 4.689A pdb=" N GLU A1601 " --> pdb=" O GLU A1597 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A1602 " --> pdb=" O ALA A1598 " (cutoff:3.500A) Proline residue: A1603 - end of helix Processing helix chain 'A' and resid 1627 through 1641 Processing helix chain 'A' and resid 1665 through 1706 removed outlier: 3.542A pdb=" N GLU A1670 " --> pdb=" O GLU A1666 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A1692 " --> pdb=" O PHE A1688 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A1693 " --> pdb=" O SER A1689 " (cutoff:3.500A) Proline residue: A1694 - end of helix Processing helix chain 'A' and resid 1709 through 1716 Processing helix chain 'A' and resid 1720 through 1749 removed outlier: 3.642A pdb=" N PHE A1749 " --> pdb=" O ILE A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1752 through 1755 No H-bonds generated for 'chain 'A' and resid 1752 through 1755' Processing helix chain 'A' and resid 1757 through 1784 Proline residue: A1761 - end of helix Proline residue: A1776 - end of helix Proline residue: A1780 - end of helix removed outlier: 4.265A pdb=" N PHE A1783 " --> pdb=" O TYR A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1813 removed outlier: 3.659A pdb=" N THR A1810 " --> pdb=" O SER A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1821 through 1829 Processing helix chain 'A' and resid 1833 through 1835 No H-bonds generated for 'chain 'A' and resid 1833 through 1835' Processing helix chain 'A' and resid 1837 through 1861 Processing helix chain 'A' and resid 1876 through 1896 removed outlier: 3.709A pdb=" N VAL A1887 " --> pdb=" O VAL A1883 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1985 Processing helix chain 'A' and resid 2034 through 2040 removed outlier: 3.732A pdb=" N LEU A2039 " --> pdb=" O LEU A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2058 Processing helix chain 'A' and resid 2073 through 2084 Processing helix chain 'A' and resid 2103 through 2119 Processing helix chain 'A' and resid 2154 through 2160 Processing helix chain 'A' and resid 2179 through 2192 removed outlier: 4.092A pdb=" N ASN A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Proline residue: A2184 - end of helix Processing helix chain 'A' and resid 2217 through 2226 Processing sheet with id= A, first strand: chain 'A' and resid 525 through 527 removed outlier: 6.273A pdb=" N ILE A 398 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU A 399 " --> pdb=" O TRP A 548 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY A 550 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY A1653 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N TYR A 569 " --> pdb=" O GLY A1653 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR A1655 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE A 571 " --> pdb=" O THR A1655 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A1657 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 958 through 960 removed outlier: 5.684A pdb=" N ILE A1113 " --> pdb=" O THR A 959 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 1156 through 1158 Processing sheet with id= D, first strand: chain 'A' and resid 1521 through 1524 removed outlier: 4.080A pdb=" N TYR A1557 " --> pdb=" O TYR A1414 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N PHE A1416 " --> pdb=" O TYR A1557 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY A1559 " --> pdb=" O PHE A1416 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER A1418 " --> pdb=" O GLY A1559 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A1561 " --> pdb=" O SER A1418 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 2122 through 2126 removed outlier: 3.960A pdb=" N CYS A2017 " --> pdb=" O LEU A2091 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU A2093 " --> pdb=" O CYS A2017 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN A2019 " --> pdb=" O LEU A2093 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP A2095 " --> pdb=" O GLN A2019 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 2206 through 2209 removed outlier: 3.772A pdb=" N LEU A2206 " --> pdb=" O MET A2169 " (cutoff:3.500A) 599 hydrogen bonds defined for protein. 1700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2207 1.31 - 1.44: 3761 1.44 - 1.56: 8002 1.56 - 1.69: 13 1.69 - 1.81: 104 Bond restraints: 14087 Sorted by residual: bond pdb=" CCP HZL A2304 " pdb=" CCQ HZL A2304 " ideal model delta sigma weight residual 1.551 1.506 0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" CAY HZL A2304 " pdb=" CBC HZL A2304 " ideal model delta sigma weight residual 1.549 1.585 -0.036 2.00e-02 2.50e+03 3.28e+00 bond pdb=" CBA HZL A2304 " pdb=" CBE HZL A2304 " ideal model delta sigma weight residual 1.343 1.307 0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" C1 NAG A2306 " pdb=" O5 NAG A2306 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" OAG HZL A2304 " pdb=" PAA HZL A2304 " ideal model delta sigma weight residual 1.669 1.704 -0.035 2.00e-02 2.50e+03 3.06e+00 ... (remaining 14082 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.85: 378 105.85 - 112.92: 7747 112.92 - 119.98: 4617 119.98 - 127.04: 6331 127.04 - 134.10: 197 Bond angle restraints: 19270 Sorted by residual: angle pdb=" CAU HZL A2304 " pdb=" CAV HZL A2304 " pdb=" CAW HZL A2304 " ideal model delta sigma weight residual 74.51 124.40 -49.89 3.00e+00 1.11e-01 2.77e+02 angle pdb=" CBR HZL A2304 " pdb=" CBV HZL A2304 " pdb=" CBY HZL A2304 " ideal model delta sigma weight residual 74.50 119.01 -44.51 3.00e+00 1.11e-01 2.20e+02 angle pdb=" CAS HZL A2304 " pdb=" CAU HZL A2304 " pdb=" CAV HZL A2304 " ideal model delta sigma weight residual 85.90 129.65 -43.75 3.00e+00 1.11e-01 2.13e+02 angle pdb=" CBM HZL A2304 " pdb=" CBR HZL A2304 " pdb=" CBV HZL A2304 " ideal model delta sigma weight residual 152.66 116.46 36.20 3.00e+00 1.11e-01 1.46e+02 angle pdb=" N PRO A 143 " pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " ideal model delta sigma weight residual 102.65 110.76 -8.11 6.80e-01 2.16e+00 1.42e+02 ... (remaining 19265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.82: 8289 33.82 - 67.63: 122 67.63 - 101.45: 42 101.45 - 135.26: 20 135.26 - 169.08: 2 Dihedral angle restraints: 8475 sinusoidal: 2938 harmonic: 5537 Sorted by residual: dihedral pdb=" CB CYS A 641 " pdb=" SG CYS A 641 " pdb=" SG CYS A1490 " pdb=" CB CYS A1490 " ideal model delta sinusoidal sigma weight residual -86.00 -29.52 -56.48 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" CAZ HZL A2304 " pdb=" CAY HZL A2304 " pdb=" CBC HZL A2304 " pdb=" CBG HZL A2304 " ideal model delta sinusoidal sigma weight residual 215.34 46.26 169.08 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CBM HZL A2304 " pdb=" CBR HZL A2304 " pdb=" CBV HZL A2304 " pdb=" CBY HZL A2304 " ideal model delta sinusoidal sigma weight residual 133.66 -6.25 139.91 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 8472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2305 0.139 - 0.279: 9 0.279 - 0.418: 0 0.418 - 0.558: 0 0.558 - 0.697: 1 Chirality restraints: 2315 Sorted by residual: chirality pdb=" C1 NAG A2307 " pdb=" ND2 ASN A 504 " pdb=" C2 NAG A2307 " pdb=" O5 NAG A2307 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 2312 not shown) Planarity restraints: 2465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 504 " 0.027 2.00e-02 2.50e+03 2.66e-02 8.87e+00 pdb=" CG ASN A 504 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 504 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 504 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A2307 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 444 " -0.006 2.00e-02 2.50e+03 2.08e-02 5.43e+00 pdb=" CG ASN A 444 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 444 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN A 444 " 0.016 2.00e-02 2.50e+03 pdb=" C1 NAG A2305 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 504 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" CG ASN A 504 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 504 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 504 " 0.012 2.00e-02 2.50e+03 ... (remaining 2462 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 131 2.62 - 3.19: 13020 3.19 - 3.76: 21537 3.76 - 4.33: 28129 4.33 - 4.90: 46265 Nonbonded interactions: 109082 Sorted by model distance: nonbonded pdb=" OD1 ASN A 338 " pdb="MG MG A2308 " model vdw 2.049 2.170 nonbonded pdb=" OG SER A 336 " pdb="MG MG A2308 " model vdw 2.135 2.170 nonbonded pdb=" OD2 ASP A1731 " pdb=" OH TYR A1779 " model vdw 2.195 2.440 nonbonded pdb=" OD1 ASN A1012 " pdb=" OG SER A1071 " model vdw 2.196 2.440 nonbonded pdb=" O TYR A 106 " pdb=" NE2 GLN A 110 " model vdw 2.206 2.520 ... (remaining 109077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 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: 6.130 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: 23.110 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 50.670 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.100 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14087 Z= 0.253 Angle : 0.969 49.892 19270 Z= 0.418 Chirality : 0.046 0.697 2315 Planarity : 0.004 0.051 2457 Dihedral : 16.197 169.077 4872 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.65 % Favored : 92.19 % Rotamer: Outliers : 0.08 % Allowed : 0.33 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1886 helix: 1.31 (0.17), residues: 995 sheet: -0.09 (0.50), residues: 109 loop : -1.73 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 697 HIS 0.003 0.001 HIS A1354 PHE 0.018 0.001 PHE A 36 TYR 0.021 0.001 TYR A1700 ARG 0.006 0.000 ARG A1824 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.717 Fit side-chains REVERT: A 449 ASN cc_start: 0.6562 (m110) cc_final: 0.6148 (m110) REVERT: A 1777 MET cc_start: 0.9137 (ttt) cc_final: 0.8894 (ttt) outliers start: 0 outliers final: 1 residues processed: 133 average time/residue: 0.9346 time to fit residues: 142.6695 Evaluate side-chains 102 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.0470 chunk 111 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A 688 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14087 Z= 0.224 Angle : 0.810 37.544 19270 Z= 0.347 Chirality : 0.043 0.428 2315 Planarity : 0.004 0.047 2457 Dihedral : 13.324 155.034 2342 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.70 % Favored : 92.14 % Rotamer: Outliers : 1.16 % Allowed : 7.45 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1886 helix: 1.32 (0.17), residues: 997 sheet: -0.09 (0.50), residues: 109 loop : -1.73 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1772 HIS 0.003 0.001 HIS A2032 PHE 0.020 0.001 PHE A 36 TYR 0.016 0.001 TYR A1700 ARG 0.005 0.000 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.437 Fit side-chains REVERT: A 757 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.5624 (mptt) REVERT: A 1777 MET cc_start: 0.9181 (ttt) cc_final: 0.8942 (ttt) outliers start: 14 outliers final: 3 residues processed: 111 average time/residue: 0.9021 time to fit residues: 115.5677 Evaluate side-chains 104 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1828 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 154 optimal weight: 0.0000 chunk 172 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A1376 GLN A1734 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14087 Z= 0.200 Angle : 0.774 30.163 19270 Z= 0.332 Chirality : 0.043 0.351 2315 Planarity : 0.004 0.046 2457 Dihedral : 11.189 165.648 2339 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.70 % Favored : 92.14 % Rotamer: Outliers : 1.74 % Allowed : 8.94 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1886 helix: 1.44 (0.17), residues: 993 sheet: 0.07 (0.50), residues: 111 loop : -1.72 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1772 HIS 0.003 0.001 HIS A1354 PHE 0.017 0.001 PHE A 36 TYR 0.013 0.001 TYR A2071 ARG 0.005 0.000 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.502 Fit side-chains REVERT: A 757 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.5600 (mptt) REVERT: A 1747 ILE cc_start: 0.9208 (tt) cc_final: 0.8993 (pp) REVERT: A 1777 MET cc_start: 0.9181 (ttt) cc_final: 0.8962 (ttt) outliers start: 21 outliers final: 7 residues processed: 113 average time/residue: 0.8820 time to fit residues: 115.0975 Evaluate side-chains 103 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1828 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 5.9990 chunk 130 optimal weight: 0.0770 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A1734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14087 Z= 0.225 Angle : 0.754 27.719 19270 Z= 0.328 Chirality : 0.043 0.306 2315 Planarity : 0.004 0.044 2457 Dihedral : 10.182 174.005 2339 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.97 % Favored : 91.93 % Rotamer: Outliers : 1.66 % Allowed : 10.76 % Favored : 87.58 % 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: 0.11 (0.20), residues: 1886 helix: 1.44 (0.17), residues: 994 sheet: 0.04 (0.50), residues: 111 loop : -1.80 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1772 HIS 0.003 0.001 HIS A1354 PHE 0.021 0.001 PHE A 36 TYR 0.015 0.001 TYR A2071 ARG 0.004 0.000 ARG A1585 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 1.568 Fit side-chains REVERT: A 757 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.5655 (mptt) outliers start: 20 outliers final: 10 residues processed: 114 average time/residue: 0.9330 time to fit residues: 122.2190 Evaluate side-chains 108 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1828 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 157 optimal weight: 0.0050 chunk 127 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 165 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14087 Z= 0.172 Angle : 0.726 25.850 19270 Z= 0.316 Chirality : 0.042 0.291 2315 Planarity : 0.004 0.044 2457 Dihedral : 9.685 167.159 2339 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.65 % Favored : 92.25 % Rotamer: Outliers : 1.57 % Allowed : 11.84 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1886 helix: 1.52 (0.17), residues: 992 sheet: 0.10 (0.51), residues: 111 loop : -1.78 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1772 HIS 0.003 0.001 HIS A1354 PHE 0.013 0.001 PHE A 36 TYR 0.012 0.001 TYR A1700 ARG 0.002 0.000 ARG A1097 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.483 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 112 average time/residue: 0.8603 time to fit residues: 111.1975 Evaluate side-chains 102 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1828 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 40.0000 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A1353 GLN A1376 GLN A1734 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14087 Z= 0.251 Angle : 0.748 25.076 19270 Z= 0.330 Chirality : 0.043 0.273 2315 Planarity : 0.004 0.043 2457 Dihedral : 9.421 155.505 2339 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.23 % Favored : 91.66 % Rotamer: Outliers : 1.99 % Allowed : 12.50 % Favored : 85.51 % 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: 0.12 (0.20), residues: 1886 helix: 1.46 (0.17), residues: 990 sheet: 0.04 (0.50), residues: 111 loop : -1.80 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1772 HIS 0.004 0.001 HIS A1354 PHE 0.018 0.001 PHE A 36 TYR 0.016 0.001 TYR A2071 ARG 0.003 0.000 ARG A1824 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.526 Fit side-chains REVERT: A 757 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.5613 (mptt) outliers start: 24 outliers final: 10 residues processed: 113 average time/residue: 0.8700 time to fit residues: 115.3414 Evaluate side-chains 106 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1828 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14087 Z= 0.243 Angle : 0.744 24.037 19270 Z= 0.329 Chirality : 0.043 0.265 2315 Planarity : 0.004 0.043 2457 Dihedral : 9.138 146.606 2339 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 1.24 % Allowed : 13.33 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1886 helix: 1.44 (0.17), residues: 987 sheet: -0.04 (0.51), residues: 109 loop : -1.77 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1772 HIS 0.003 0.001 HIS A1011 PHE 0.019 0.001 PHE A 36 TYR 0.015 0.001 TYR A2071 ARG 0.008 0.000 ARG A2038 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.392 Fit side-chains REVERT: A 637 MET cc_start: 0.9011 (mtt) cc_final: 0.8578 (mtt) REVERT: A 757 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.5613 (mptt) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 0.8362 time to fit residues: 101.0201 Evaluate side-chains 102 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1828 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.0370 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A1376 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14087 Z= 0.160 Angle : 0.719 23.615 19270 Z= 0.314 Chirality : 0.041 0.278 2315 Planarity : 0.004 0.043 2457 Dihedral : 8.747 146.217 2339 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.59 % Favored : 92.30 % Rotamer: Outliers : 0.99 % Allowed : 13.74 % Favored : 85.26 % 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: 0.28 (0.20), residues: 1886 helix: 1.61 (0.17), residues: 973 sheet: 0.10 (0.51), residues: 109 loop : -1.67 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1772 HIS 0.003 0.001 HIS A1354 PHE 0.013 0.001 PHE A1630 TYR 0.013 0.001 TYR A1735 ARG 0.006 0.000 ARG A2038 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.625 Fit side-chains REVERT: A 420 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: A 637 MET cc_start: 0.8986 (mtt) cc_final: 0.8539 (mtt) outliers start: 12 outliers final: 8 residues processed: 107 average time/residue: 0.8690 time to fit residues: 107.4868 Evaluate side-chains 102 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1828 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 103 optimal weight: 40.0000 chunk 74 optimal weight: 0.0040 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 110 GLN A 413 ASN A1376 GLN A1734 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14087 Z= 0.275 Angle : 0.755 23.834 19270 Z= 0.337 Chirality : 0.043 0.260 2315 Planarity : 0.004 0.043 2457 Dihedral : 8.617 135.914 2339 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.91 % Favored : 91.98 % Rotamer: Outliers : 1.16 % Allowed : 13.66 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1886 helix: 1.42 (0.17), residues: 980 sheet: 0.01 (0.50), residues: 114 loop : -1.73 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1772 HIS 0.004 0.001 HIS A1011 PHE 0.019 0.001 PHE A 36 TYR 0.017 0.001 TYR A2071 ARG 0.008 0.000 ARG A2038 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.524 Fit side-chains REVERT: A 280 MET cc_start: 0.7928 (mmt) cc_final: 0.7644 (mmp) REVERT: A 637 MET cc_start: 0.9059 (mtt) cc_final: 0.8677 (mtt) REVERT: A 746 MET cc_start: 0.8661 (mpt) cc_final: 0.7202 (mpt) REVERT: A 757 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.5594 (mptt) outliers start: 14 outliers final: 7 residues processed: 106 average time/residue: 0.8561 time to fit residues: 105.5476 Evaluate side-chains 103 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.9980 chunk 181 optimal weight: 0.3980 chunk 110 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 15 optimal weight: 40.0000 chunk 117 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14087 Z= 0.262 Angle : 0.758 23.747 19270 Z= 0.337 Chirality : 0.043 0.259 2315 Planarity : 0.004 0.044 2457 Dihedral : 8.508 132.908 2339 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.14 % Rotamer: Outliers : 0.91 % Allowed : 13.99 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1886 helix: 1.37 (0.17), residues: 983 sheet: -0.01 (0.50), residues: 114 loop : -1.73 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 697 HIS 0.003 0.001 HIS A1354 PHE 0.018 0.001 PHE A 36 TYR 0.016 0.001 TYR A1735 ARG 0.008 0.000 ARG A2038 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 1.697 Fit side-chains REVERT: A 280 MET cc_start: 0.7956 (mmt) cc_final: 0.7698 (mmp) REVERT: A 637 MET cc_start: 0.9075 (mtt) cc_final: 0.8697 (mtt) REVERT: A 746 MET cc_start: 0.8645 (mpt) cc_final: 0.7165 (mpt) REVERT: A 757 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.5581 (mptt) outliers start: 11 outliers final: 8 residues processed: 105 average time/residue: 0.8489 time to fit residues: 103.5794 Evaluate side-chains 105 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1689 SER Chi-restraints excluded: chain A residue 1828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.1980 chunk 151 optimal weight: 4.9990 chunk 63 optimal weight: 0.0010 chunk 155 optimal weight: 3.9990 chunk 19 optimal weight: 50.0000 chunk 27 optimal weight: 0.5980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.114630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081379 restraints weight = 55516.753| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.62 r_work: 0.3108 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14087 Z= 0.172 Angle : 0.732 23.543 19270 Z= 0.323 Chirality : 0.042 0.274 2315 Planarity : 0.004 0.043 2457 Dihedral : 8.267 127.832 2339 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.54 % Favored : 92.35 % Rotamer: Outliers : 0.91 % Allowed : 13.91 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1886 helix: 1.48 (0.17), residues: 972 sheet: 0.12 (0.51), residues: 114 loop : -1.66 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1772 HIS 0.003 0.001 HIS A1608 PHE 0.014 0.001 PHE A 36 TYR 0.017 0.001 TYR A1735 ARG 0.007 0.000 ARG A2038 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3812.79 seconds wall clock time: 69 minutes 47.84 seconds (4187.84 seconds total)