Starting phenix.real_space_refine on Thu Nov 16 15:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkp_23409/11_2023/7lkp_23409_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkp_23409/11_2023/7lkp_23409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkp_23409/11_2023/7lkp_23409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkp_23409/11_2023/7lkp_23409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkp_23409/11_2023/7lkp_23409_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkp_23409/11_2023/7lkp_23409_updated.pdb" } resolution = 3.27 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= -0.001 sd= 0.062 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10278 2.51 5 N 2564 2.21 5 O 2863 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "A GLU 814": "OE1" <-> "OE2" Residue "A GLU 833": "OE1" <-> "OE2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A GLU 995": "OE1" <-> "OE2" Residue "A ARG 1002": "NH1" <-> "NH2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A GLU 1043": "OE1" <-> "OE2" Residue "A GLU 1047": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1087": "OE1" <-> "OE2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "A ARG 1111": "NH1" <-> "NH2" Residue "A GLU 1122": "OE1" <-> "OE2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A GLU 1207": "OE1" <-> "OE2" Residue "A GLU 1228": "OE1" <-> "OE2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "A GLU 1252": "OE1" <-> "OE2" Residue "A GLU 1271": "OE1" <-> "OE2" Residue "A GLU 1421": "OE1" <-> "OE2" Residue "A ARG 1443": "NH1" <-> "NH2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "A GLU 1494": "OE1" <-> "OE2" Residue "A ARG 1514": "NH1" <-> "NH2" Residue "A GLU 1520": "OE1" <-> "OE2" Residue "A ARG 1528": "NH1" <-> "NH2" Residue "A ARG 1543": "NH1" <-> "NH2" Residue "A ARG 1596": "NH1" <-> "NH2" Residue "A GLU 1597": "OE1" <-> "OE2" Residue "A GLU 1601": "OE1" <-> "OE2" Residue "A GLU 1610": "OE1" <-> "OE2" Residue "A GLU 1666": "OE1" <-> "OE2" Residue "A GLU 1670": "OE1" <-> "OE2" Residue "A ARG 1705": "NH1" <-> "NH2" Residue "A GLU 1814": "OE1" <-> "OE2" Residue "A GLU 1864": "OE1" <-> "OE2" Residue "A GLU 1912": "OE1" <-> "OE2" Residue "A GLU 1917": "OE1" <-> "OE2" Residue "A GLU 1923": "OE1" <-> "OE2" Residue "A ARG 1927": "NH1" <-> "NH2" Residue "A ARG 1963": "NH1" <-> "NH2" Residue "A GLU 1966": "OE1" <-> "OE2" Residue "A GLU 2009": "OE1" <-> "OE2" Residue "A ARG 2030": "NH1" <-> "NH2" Residue "A GLU 2031": "OE1" <-> "OE2" Residue "A ARG 2038": "NH1" <-> "NH2" Residue "A ARG 2077": "NH1" <-> "NH2" Residue "A ARG 2107": "NH1" <-> "NH2" Residue "A ARG 2118": "NH1" <-> "NH2" Residue "A GLU 2119": "OE1" <-> "OE2" Residue "A ARG 2121": "NH1" <-> "NH2" Residue "A GLU 2132": "OE1" <-> "OE2" Residue "A ARG 2139": "NH1" <-> "NH2" Residue "A ARG 2149": "NH1" <-> "NH2" Residue "A GLU 2200": "OE1" <-> "OE2" Residue "A ARG 2201": "NH1" <-> "NH2" Residue "A GLU 2233": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 15789 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1941, 15274 Classifications: {'peptide': 1941} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 102, 'TRANS': 1838} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 117 Chain: "B" 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 chiralities: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 415 Unusual residues: {'AJP': 1, 'CLR': 7, 'NAG': 6, 'POV': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'POV:plan-3': 7, 'POV:plan-2': 7, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 8.82, per 1000 atoms: 0.56 Number of scatterers: 15789 At special positions: 0 Unit cell: (85.49, 99.91, 210.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2863 8.00 N 2564 7.00 C 10278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 A1444 " - pdb=" SG CYS A1455 " distance=2.04 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.02 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=4, symmetry=0 Links applied BETA1-3 " BMA C 3 " - " BMA C 4 " 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 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A2301 " - " ASN A 444 " " NAG A2302 " - " ASN A 504 " " NAG A2303 " - " ASN A1469 " " NAG A2304 " - " ASN A1588 " " NAG A2305 " - " ASN A1662 " " NAG A2306 " - " ASN A 98 " " NAG B 1 " - " ASN A 415 " " NAG C 1 " - " ASN A1529 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.58 Conformation dependent library (CDL) restraints added in 2.8 seconds 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 9 sheets defined 50.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.95 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 Processing helix chain 'A' and resid 24 through 45 Proline residue: A 32 - end of helix 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 74 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 136 Processing helix chain 'A' and resid 275 through 289 Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.783A pdb=" N GLN A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 305' Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.564A pdb=" N ASP A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 368 through 377 Processing helix chain 'A' and resid 385 through 395 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'A' and resid 416 through 443 removed outlier: 3.819A pdb=" N GLU A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 4.083A 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 458 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 499 through 519 removed outlier: 4.817A pdb=" N CYS A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 544 removed outlier: 3.660A pdb=" N SER A 540 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.569A pdb=" N ARG A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Proline residue: A 656 - end of helix removed outlier: 4.174A pdb=" N TRP A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.638A pdb=" N LYS A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 689 Processing helix chain 'A' and resid 694 through 722 WARNING: missing atoms! Processing helix chain 'A' and resid 730 through 754 removed outlier: 3.776A pdb=" N THR A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 780 removed outlier: 4.690A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Proline residue: A 775 - end of helix removed outlier: 3.987A pdb=" N LEU A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 removed outlier: 4.128A pdb=" N LEU A 796 " --> pdb=" O LYS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 814 removed outlier: 4.064A pdb=" N TYR A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 860 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 1000 through 1003 No H-bonds generated for 'chain 'A' and resid 1000 through 1003' Processing helix chain 'A' and resid 1020 through 1031 removed outlier: 3.658A pdb=" N LYS A1031 " --> pdb=" O TYR A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1049 Processing helix chain 'A' and resid 1052 through 1054 No H-bonds generated for 'chain 'A' and resid 1052 through 1054' Processing helix chain 'A' and resid 1064 through 1074 Processing helix chain 'A' and resid 1077 through 1079 No H-bonds generated for 'chain 'A' and resid 1077 through 1079' Processing helix chain 'A' and resid 1094 through 1106 Processing helix chain 'A' and resid 1121 through 1125 Processing helix chain 'A' and resid 1144 through 1148 Processing helix chain 'A' and resid 1206 through 1215 Processing helix chain 'A' and resid 1240 through 1252 Processing helix chain 'A' and resid 1269 through 1276 Processing helix chain 'A' and resid 1349 through 1368 removed outlier: 3.950A pdb=" N ARG A1368 " --> pdb=" O GLN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1391 removed outlier: 5.276A pdb=" N LEU A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Proline residue: A1380 - end of helix Processing helix chain 'A' and resid 1407 through 1410 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: 3.685A pdb=" N SER A1545 " --> pdb=" O LEU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1586 Processing helix chain 'A' and resid 1593 through 1598 Processing helix chain 'A' and resid 1602 through 1607 Processing helix chain 'A' and resid 1626 through 1640 Processing helix chain 'A' and resid 1665 through 1706 removed outlier: 4.360A pdb=" N LEU A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A1675 " --> pdb=" O ILE A1671 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL A1693 " --> pdb=" O SER A1689 " (cutoff:3.500A) Proline residue: A1694 - end of helix removed outlier: 3.763A pdb=" N PHE A1697 " --> pdb=" O VAL A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1716 Processing helix chain 'A' and resid 1720 through 1748 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 1760 through 1784 Proline residue: A1776 - end of helix Proline residue: A1780 - end of helix removed outlier: 4.462A pdb=" N PHE A1783 " --> pdb=" O TYR A1779 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A1784 " --> pdb=" O PRO A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1815 removed outlier: 4.274A pdb=" N THR A1810 " --> pdb=" O SER A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1835 removed outlier: 3.643A pdb=" N ILE A1834 " --> pdb=" O ARG A1830 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A1835 " --> pdb=" O LYS A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1861 removed outlier: 3.601A pdb=" N LEU A1841 " --> pdb=" O PRO A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1877 through 1898 Processing helix chain 'A' and resid 1919 through 1929 Processing helix chain 'A' and resid 1978 through 1986 Processing helix chain 'A' and resid 2008 through 2012 Processing helix chain 'A' and resid 2029 through 2040 removed outlier: 3.901A pdb=" N LEU A2033 " --> pdb=" O GLY A2029 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2057 removed outlier: 4.818A pdb=" N GLU A2048 " --> pdb=" O GLU A2045 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A2057 " --> pdb=" O SER A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2073 through 2084 Processing helix chain 'A' and resid 2106 through 2119 Processing helix chain 'A' and resid 2130 through 2136 Processing helix chain 'A' and resid 2154 through 2160 Processing helix chain 'A' and resid 2179 through 2192 Proline residue: A2184 - end of helix removed outlier: 3.994A pdb=" N ASN A2192 " --> pdb=" O PHE A2189 " (cutoff:3.500A) Processing helix chain 'A' and resid 2215 through 2224 Processing helix chain 'A' and resid 2241 through 2252 Processing sheet with id= A, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.610A pdb=" N ILE A1615 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N GLN A 635 " --> pdb=" O ILE A1615 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL A1617 " --> pdb=" O GLN A 635 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N TYR A1414 " --> pdb=" O TYR A1557 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY A1559 " --> pdb=" O TYR A1414 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE A1416 " --> pdb=" O GLY A1559 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER A1561 " --> pdb=" O PHE A1416 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 525 through 527 removed outlier: 6.370A pdb=" N ILE A 398 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA A 549 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLY A1653 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N TYR A 569 " --> pdb=" O GLY A1653 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A1655 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE A 571 " --> pdb=" O THR A1655 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A1657 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 929 through 932 removed outlier: 3.845A pdb=" N LEU A 988 " --> pdb=" O CYS A 930 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 986 " --> pdb=" O LYS A 932 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 6.667A pdb=" N THR A 959 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A1129 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU A 962 " --> pdb=" O ARG A1129 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A1131 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A1140 " --> pdb=" O ILE A1132 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A1134 " --> pdb=" O LEU A1138 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1223 through 1225 removed outlier: 3.512A pdb=" N ILE A1225 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A1261 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1938 through 1941 Processing sheet with id= G, first strand: chain 'A' and resid 2014 through 2016 removed outlier: 7.305A pdb=" N LEU A2091 " --> pdb=" O GLY A2015 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA A2122 " --> pdb=" O VAL A2092 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 2231 through 2237 removed outlier: 3.612A pdb=" N GLU A2232 " --> pdb=" O LYS A2170 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS A2170 " --> pdb=" O GLU A2232 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR A2234 " --> pdb=" O THR A2168 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A2168 " --> pdb=" O TYR A2234 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL A2236 " --> pdb=" O ILE A2166 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A2166 " --> pdb=" O VAL A2236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A2200 " --> pdb=" O GLN A2207 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLN A2209 " --> pdb=" O GLN A2198 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLN A2198 " --> pdb=" O GLN A2209 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2140 through 2143 653 hydrogen bonds defined for protein. 1890 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: 6.65 Time building geometry restraints manager: 7.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3011 1.33 - 1.45: 3953 1.45 - 1.58: 9090 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 16189 Sorted by residual: bond pdb=" C29 POV A2317 " pdb="C210 POV A2317 " ideal model delta sigma weight residual 1.333 1.518 -0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C TYR A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.330 1.374 -0.044 1.25e-02 6.40e+03 1.27e+01 bond pdb=" N SER A 281 " pdb=" CA SER A 281 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.04e-02 9.25e+03 9.67e+00 ... (remaining 16184 not shown) Histogram of bond angle deviations from ideal: 97.40 - 104.78: 369 104.78 - 112.15: 8231 112.15 - 119.53: 5517 119.53 - 126.91: 7676 126.91 - 134.29: 235 Bond angle restraints: 22028 Sorted by residual: angle pdb=" N PRO A 492 " pdb=" CA PRO A 492 " pdb=" CB PRO A 492 " ideal model delta sigma weight residual 103.25 110.61 -7.36 1.05e+00 9.07e-01 4.91e+01 angle pdb=" C SER A 281 " pdb=" N PRO A 282 " pdb=" CA PRO A 282 " ideal model delta sigma weight residual 119.05 126.62 -7.57 1.11e+00 8.12e-01 4.65e+01 angle pdb=" C28 POV A2317 " pdb=" C29 POV A2317 " pdb="C210 POV A2317 " ideal model delta sigma weight residual 127.79 108.50 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C29 POV A2317 " pdb="C210 POV A2317 " pdb="C211 POV A2317 " ideal model delta sigma weight residual 127.67 108.42 19.25 3.00e+00 1.11e-01 4.12e+01 angle pdb=" C TYR A 326 " pdb=" N PRO A 327 " pdb=" CA PRO A 327 " ideal model delta sigma weight residual 120.21 125.76 -5.55 9.60e-01 1.09e+00 3.34e+01 ... (remaining 22023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.48: 8677 25.48 - 50.95: 681 50.95 - 76.43: 41 76.43 - 101.90: 17 101.90 - 127.38: 6 Dihedral angle restraints: 9422 sinusoidal: 3798 harmonic: 5624 Sorted by residual: dihedral pdb=" CB CYS A 370 " pdb=" SG CYS A 370 " pdb=" SG CYS A 519 " pdb=" CB CYS A 519 " ideal model delta sinusoidal sigma weight residual 93.00 169.86 -76.86 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CB CYS A1444 " pdb=" SG CYS A1444 " pdb=" SG CYS A1455 " pdb=" CB CYS A1455 " ideal model delta sinusoidal sigma weight residual 93.00 151.60 -58.60 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 81 " pdb=" CB CYS A 81 " ideal model delta sinusoidal sigma weight residual -86.00 -142.66 56.66 1 1.00e+01 1.00e-02 4.32e+01 ... (remaining 9419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.186: 2532 1.186 - 2.372: 0 2.372 - 3.559: 0 3.559 - 4.745: 6 4.745 - 5.931: 23 Chirality restraints: 2561 Sorted by residual: chirality pdb=" C12 AJP A2310 " pdb=" C07 AJP A2310 " pdb=" C11 AJP A2310 " pdb=" C13 AJP A2310 " both_signs ideal model delta sigma weight residual False 3.01 -2.92 5.93 2.00e-01 2.50e+01 8.79e+02 chirality pdb=" C20 AJP A2310 " pdb=" C15 AJP A2310 " pdb=" C19 AJP A2310 " pdb=" C21 AJP A2310 " both_signs ideal model delta sigma weight residual False 2.96 -2.88 5.83 2.00e-01 2.50e+01 8.51e+02 chirality pdb=" C07 AJP A2310 " pdb=" C06 AJP A2310 " pdb=" C08 AJP A2310 " pdb=" C12 AJP A2310 " both_signs ideal model delta sigma weight residual False -2.73 2.69 -5.42 2.00e-01 2.50e+01 7.34e+02 ... (remaining 2558 not shown) Planarity restraints: 2722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A2317 " -0.126 2.00e-02 2.50e+03 1.26e-01 1.59e+02 pdb=" C29 POV A2317 " 0.126 2.00e-02 2.50e+03 pdb="C210 POV A2317 " 0.126 2.00e-02 2.50e+03 pdb="C211 POV A2317 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.005 2.00e-02 2.50e+03 2.61e-02 8.51e+00 pdb=" CG ASN A 98 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG A2306 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1494 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" CD GLU A1494 " 0.048 2.00e-02 2.50e+03 pdb=" OE1 GLU A1494 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU A1494 " -0.017 2.00e-02 2.50e+03 ... (remaining 2719 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 120 2.54 - 3.13: 13001 3.13 - 3.72: 24072 3.72 - 4.31: 31573 4.31 - 4.90: 53350 Nonbonded interactions: 122116 Sorted by model distance: nonbonded pdb=" NE2 GLN A1475 " pdb=" CD LYS A1476 " model vdw 1.954 3.520 nonbonded pdb=" CG LYS A2172 " pdb=" OE2 GLU A2232 " model vdw 1.992 3.440 nonbonded pdb=" OD2 ASP A1731 " pdb=" OH TYR A1779 " model vdw 2.075 2.440 nonbonded pdb=" CD1 LEU A2178 " pdb=" N LEU A2179 " model vdw 2.086 3.540 nonbonded pdb=" OD1 ASN A 965 " pdb=" OG1 THR A 970 " model vdw 2.110 2.440 ... (remaining 122111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 10.240 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 45.230 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 : 0.006 0.185 16189 Z= 0.408 Angle : 0.988 19.286 22028 Z= 0.565 Chirality : 0.534 5.931 2561 Planarity : 0.005 0.126 2714 Dihedral : 16.725 127.378 5772 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 0.60 % Allowed : 1.99 % Favored : 97.40 % 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: -0.89 (0.19), residues: 1923 helix: 0.84 (0.16), residues: 1045 sheet: -1.90 (0.39), residues: 172 loop : -2.49 (0.22), residues: 706 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 283 time to evaluate : 1.856 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 4 residues processed: 291 average time/residue: 0.3146 time to fit residues: 132.5935 Evaluate side-chains 198 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 194 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1466 time to fit residues: 3.5454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 375 GLN A 536 GLN A1029 GLN ** A1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1356 GLN ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1621 ASN A1899 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16189 Z= 0.259 Angle : 0.947 35.426 22028 Z= 0.401 Chirality : 0.082 2.170 2561 Planarity : 0.005 0.062 2714 Dihedral : 7.252 95.848 2196 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 1.21 % Allowed : 13.65 % Favored : 85.14 % 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: -0.64 (0.19), residues: 1923 helix: 1.02 (0.16), residues: 1043 sheet: -1.59 (0.38), residues: 179 loop : -2.38 (0.22), residues: 701 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. outliers start: 20 outliers final: 18 residues processed: 218 average time/residue: 0.2655 time to fit residues: 89.1194 Evaluate side-chains 205 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1499 time to fit residues: 7.4623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 157 optimal weight: 0.1980 chunk 175 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 375 GLN ** A1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 HIS ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16189 Z= 0.200 Angle : 0.867 33.834 22028 Z= 0.364 Chirality : 0.081 2.160 2561 Planarity : 0.004 0.058 2714 Dihedral : 6.225 59.656 2196 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 1.27 % Allowed : 16.61 % Favored : 82.13 % 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: -0.46 (0.20), residues: 1923 helix: 1.11 (0.16), residues: 1051 sheet: -1.42 (0.39), residues: 177 loop : -2.26 (0.22), residues: 695 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. outliers start: 21 outliers final: 9 residues processed: 220 average time/residue: 0.2686 time to fit residues: 91.2962 Evaluate side-chains 191 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1580 time to fit residues: 4.9858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 84 optimal weight: 0.7980 chunk 118 optimal weight: 0.3980 chunk 177 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 338 ASN A 413 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16189 Z= 0.186 Angle : 0.843 33.943 22028 Z= 0.351 Chirality : 0.079 2.074 2561 Planarity : 0.004 0.062 2714 Dihedral : 5.735 56.924 2196 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 1.27 % Allowed : 19.08 % Favored : 79.65 % 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: -0.30 (0.20), residues: 1923 helix: 1.21 (0.17), residues: 1053 sheet: -1.29 (0.40), residues: 169 loop : -2.16 (0.22), residues: 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.720 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. outliers start: 21 outliers final: 16 residues processed: 211 average time/residue: 0.2691 time to fit residues: 88.3269 Evaluate side-chains 193 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1499 time to fit residues: 7.0009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.0670 chunk 106 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16189 Z= 0.196 Angle : 0.835 33.944 22028 Z= 0.349 Chirality : 0.079 2.055 2561 Planarity : 0.004 0.064 2714 Dihedral : 5.498 59.444 2196 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 0.97 % Allowed : 20.11 % Favored : 78.93 % 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: -0.24 (0.20), residues: 1923 helix: 1.26 (0.17), residues: 1052 sheet: -1.35 (0.39), residues: 174 loop : -2.10 (0.22), residues: 697 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 1.985 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 7 residues processed: 200 average time/residue: 0.2694 time to fit residues: 84.0960 Evaluate side-chains 186 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 179 time to evaluate : 1.714 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1640 time to fit residues: 4.4221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 0.0980 chunk 168 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 0.0000 chunk 46 optimal weight: 0.9980 chunk 187 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1727 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16189 Z= 0.179 Angle : 0.825 33.973 22028 Z= 0.342 Chirality : 0.078 2.047 2561 Planarity : 0.004 0.066 2714 Dihedral : 5.317 59.478 2196 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 1.33 % Allowed : 21.32 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1923 helix: 1.31 (0.16), residues: 1057 sheet: -1.20 (0.40), residues: 172 loop : -2.06 (0.22), residues: 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.641 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. outliers start: 22 outliers final: 10 residues processed: 199 average time/residue: 0.2653 time to fit residues: 82.4452 Evaluate side-chains 183 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1512 time to fit residues: 5.3228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 186 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16189 Z= 0.216 Angle : 0.834 34.017 22028 Z= 0.349 Chirality : 0.078 2.033 2561 Planarity : 0.004 0.068 2714 Dihedral : 5.306 58.178 2196 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 0.72 % Allowed : 22.22 % Favored : 77.05 % 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: 1923 helix: 1.43 (0.17), residues: 1037 sheet: -1.22 (0.39), residues: 172 loop : -2.02 (0.22), residues: 714 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 1.637 Fit side-chains TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. outliers start: 12 outliers final: 4 residues processed: 196 average time/residue: 0.2914 time to fit residues: 90.0407 Evaluate side-chains 181 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1653 time to fit residues: 4.0091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 0.0010 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16189 Z= 0.194 Angle : 0.830 33.998 22028 Z= 0.344 Chirality : 0.078 2.030 2561 Planarity : 0.004 0.055 2714 Dihedral : 5.213 57.243 2196 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 0.60 % Allowed : 22.95 % Favored : 76.45 % 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: 1923 helix: 1.45 (0.17), residues: 1036 sheet: -1.18 (0.39), residues: 172 loop : -1.99 (0.22), residues: 715 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 184 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 8 residues processed: 191 average time/residue: 0.2587 time to fit residues: 77.3861 Evaluate side-chains 182 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1518 time to fit residues: 4.5746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 179 optimal weight: 0.0470 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 136 optimal weight: 0.0050 chunk 53 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.5292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16189 Z= 0.181 Angle : 0.834 33.969 22028 Z= 0.346 Chirality : 0.078 2.031 2561 Planarity : 0.004 0.051 2714 Dihedral : 5.140 56.732 2196 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.63 % Rotamer: Outliers : 0.36 % Allowed : 23.43 % Favored : 76.21 % 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: 1923 helix: 1.48 (0.17), residues: 1041 sheet: -1.06 (0.39), residues: 166 loop : -1.97 (0.22), residues: 716 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 177 time to evaluate : 1.755 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 2 residues processed: 182 average time/residue: 0.2698 time to fit residues: 77.2254 Evaluate side-chains 175 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 1.718 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1466 time to fit residues: 2.9507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 177 optimal weight: 0.0970 chunk 153 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16189 Z= 0.173 Angle : 0.825 33.927 22028 Z= 0.341 Chirality : 0.078 2.030 2561 Planarity : 0.004 0.048 2714 Dihedral : 5.071 56.164 2196 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.68 % Rotamer: Outliers : 0.36 % Allowed : 23.07 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1923 helix: 1.51 (0.17), residues: 1044 sheet: -0.99 (0.39), residues: 166 loop : -1.95 (0.22), residues: 713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 4 residues processed: 188 average time/residue: 0.2702 time to fit residues: 79.6575 Evaluate side-chains 177 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 1.846 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1692 time to fit residues: 3.7657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.8980 chunk 47 optimal weight: 0.2980 chunk 141 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 42 optimal weight: 0.0870 chunk 154 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 135 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.169675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136053 restraints weight = 19393.906| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.07 r_work: 0.3498 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16189 Z= 0.168 Angle : 0.816 33.882 22028 Z= 0.337 Chirality : 0.078 2.029 2561 Planarity : 0.004 0.047 2714 Dihedral : 5.003 55.730 2196 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.21 % Favored : 95.74 % Rotamer: Outliers : 0.18 % Allowed : 23.37 % Favored : 76.45 % 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: 1923 helix: 1.52 (0.17), residues: 1044 sheet: -0.95 (0.39), residues: 168 loop : -1.95 (0.22), residues: 711 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3390.43 seconds wall clock time: 62 minutes 50.02 seconds (3770.02 seconds total)