Starting phenix.real_space_refine (version: dev) on Mon Feb 20 09:11:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2023/7ela_31178.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2023/7ela_31178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2023/7ela_31178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2023/7ela_31178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2023/7ela_31178.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2023/7ela_31178.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B GLU 43": "OE1" <-> "OE2" Residue "A GLU 2": "OE1" <-> "OE2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A ASP 10": "OD1" <-> "OD2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 398": "NH1" <-> "NH2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 487": "OD1" <-> "OD2" Residue "A GLU 497": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A ARG 718": "NH1" <-> "NH2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A ARG 1133": "NH1" <-> "NH2" Residue "A GLU 1134": "OE1" <-> "OE2" Residue "A TYR 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1151": "OD1" <-> "OD2" Residue "A TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1172": "OE1" <-> "OE2" Residue "A ARG 1226": "NH1" <-> "NH2" Residue "A TYR 1228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1272": "OE1" <-> "OE2" Residue "A ASP 1273": "OD1" <-> "OD2" Residue "A TYR 1276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1293": "OD1" <-> "OD2" Residue "A ARG 1312": "NH1" <-> "NH2" Residue "A ASP 1333": "OD1" <-> "OD2" Residue "A ARG 1355": "NH1" <-> "NH2" Residue "A TYR 1362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1395": "OE1" <-> "OE2" Residue "A PHE 1460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1467": "OD1" <-> "OD2" Residue "A ARG 1469": "NH1" <-> "NH2" Residue "A ARG 1476": "NH1" <-> "NH2" Residue "A GLU 1514": "OE1" <-> "OE2" Residue "A PHE 1515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1533": "OE1" <-> "OE2" Residue "A GLU 1542": "OE1" <-> "OE2" Residue "A ASP 1544": "OD1" <-> "OD2" Residue "A GLU 1546": "OE1" <-> "OE2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1632": "NH1" <-> "NH2" Residue "A ARG 1667": "NH1" <-> "NH2" Residue "A PHE 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1700": "OE1" <-> "OE2" Residue "A ASP 1708": "OD1" <-> "OD2" Residue "A ASP 1724": "OD1" <-> "OD2" Residue "A TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1751": "NH1" <-> "NH2" Residue "A TYR 1753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1758": "OE1" <-> "OE2" Residue "A GLU 1793": "OE1" <-> "OE2" Residue "A ARG 1806": "NH1" <-> "NH2" Residue "A GLU 1807": "OE1" <-> "OE2" Residue "A TYR 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1818": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11791 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 375 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 3} Chain: "A" Number of atoms: 11264 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1402, 11250 Classifications: {'peptide': 1402} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 46, 'TRANS': 1355} Chain breaks: 11 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 1402, 11250 Classifications: {'peptide': 1402} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 46, 'TRANS': 1355} Chain breaks: 11 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 11448 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 55 SG CYS B 31 75.022 70.911 96.200 1.00 59.29 S ATOM 76 SG CYS B 34 77.728 67.648 96.289 1.00 53.18 S ATOM 207 SG CYS B 50 77.976 71.670 97.807 1.00 71.19 S ATOM 229 SG CYS B 53 77.915 71.242 94.375 1.00 71.71 S ATOM 155 SG CYS B 44 70.342 79.282 92.118 1.00 81.15 S ATOM 308 SG CYS B 64 72.367 77.979 89.642 1.00 84.11 S ATOM 329 SG CYS B 67 69.032 78.503 89.041 1.00 90.04 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A1392 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A1392 " occ=0.50 Time building chain proxies: 12.00, per 1000 atoms: 1.02 Number of scatterers: 11791 At special positions: 0 Unit cell: (115, 99, 122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Mn 1 24.99 S 80 16.00 P 7 15.00 O 2226 8.00 N 1978 7.00 C 7497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1692 " - pdb=" SG CYS A1792 " 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 Time building additional restraints: 5.21 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 53 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 50 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 31 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 34 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 47 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 67 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 44 " Number of angles added : 9 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 13 sheets defined 55.9% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 34 through 59 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 108 through 132 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 179 through 191 Processing helix chain 'A' and resid 211 through 221 removed outlier: 4.130A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 252 removed outlier: 3.776A pdb=" N LYS A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 340 through 363 removed outlier: 3.659A pdb=" N ARG A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.872A pdb=" N VAL A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 436 Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.518A pdb=" N LYS A 445 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'A' and resid 588 through 603 removed outlier: 3.850A pdb=" N GLN A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 603 " --> pdb=" O MET A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 removed outlier: 4.393A pdb=" N ASN A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 612 through 630 Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.697A pdb=" N VAL A 650 " --> pdb=" O ILE A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 663 Processing helix chain 'A' and resid 670 through 686 Processing helix chain 'A' and resid 693 through 707 Processing helix chain 'A' and resid 708 through 711 Processing helix chain 'A' and resid 717 through 737 Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 748 through 763 removed outlier: 3.607A pdb=" N LEU A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 795 Processing helix chain 'A' and resid 1139 through 1160 Processing helix chain 'A' and resid 1167 through 1184 Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 3.534A pdb=" N MET A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A1200 " --> pdb=" O TRP A1196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1195 through 1200' Processing helix chain 'A' and resid 1201 through 1211 Processing helix chain 'A' and resid 1225 through 1238 Processing helix chain 'A' and resid 1244 through 1261 Processing helix chain 'A' and resid 1269 through 1280 Processing helix chain 'A' and resid 1299 through 1323 Processing helix chain 'A' and resid 1340 through 1350 Processing helix chain 'A' and resid 1350 through 1368 Processing helix chain 'A' and resid 1398 through 1409 removed outlier: 3.530A pdb=" N PHE A1402 " --> pdb=" O LEU A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1433 Processing helix chain 'A' and resid 1435 through 1453 removed outlier: 3.581A pdb=" N ALA A1453 " --> pdb=" O LEU A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1490 through 1508 removed outlier: 3.573A pdb=" N LYS A1494 " --> pdb=" O ASP A1490 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A1508 " --> pdb=" O ASN A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1520 removed outlier: 3.732A pdb=" N THR A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASN A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1536 removed outlier: 3.905A pdb=" N LYS A1529 " --> pdb=" O LEU A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1586 removed outlier: 3.814A pdb=" N ILE A1586 " --> pdb=" O ILE A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1626 Processing helix chain 'A' and resid 1640 through 1650 Processing helix chain 'A' and resid 1678 through 1681 Processing helix chain 'A' and resid 1686 through 1701 Processing helix chain 'A' and resid 1703 through 1707 Processing helix chain 'A' and resid 1744 through 1753 Processing helix chain 'A' and resid 1753 through 1759 Processing helix chain 'A' and resid 1782 through 1791 removed outlier: 4.281A pdb=" N ASP A1789 " --> pdb=" O CYS A1785 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A1790 " --> pdb=" O VAL A1786 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN A1791 " --> pdb=" O ALA A1787 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1819 removed outlier: 3.590A pdb=" N ARG A1818 " --> pdb=" O SER A1814 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A1819 " --> pdb=" O SER A1815 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1814 through 1819' Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 6.552A pdb=" N LEU A 98 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 62 removed outlier: 7.471A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 208 removed outlier: 6.152A pdb=" N LEU A 207 " --> pdb=" O TYR A1109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA6, first strand: chain 'A' and resid 373 through 375 Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 542 removed outlier: 6.411A pdb=" N LYS A 560 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR A 576 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR A 562 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER A 574 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 564 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1133 through 1138 removed outlier: 3.584A pdb=" N LEU A1123 " --> pdb=" O GLU A1242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1383 through 1385 Processing sheet with id=AB1, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AB2, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 3.539A pdb=" N VAL A1631 " --> pdb=" O LEU A1639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1710 through 1711 Processing sheet with id=AB4, first strand: chain 'A' and resid 1725 through 1728 removed outlier: 3.709A pdb=" N VAL A1812 " --> pdb=" O PHE A1726 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3623 1.34 - 1.46: 1716 1.46 - 1.57: 6562 1.57 - 1.69: 13 1.69 - 1.81: 117 Bond restraints: 12031 Sorted by residual: bond pdb=" N VAL A1468 " pdb=" CA VAL A1468 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.40e+00 bond pdb=" N THR A1466 " pdb=" CA THR A1466 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.34e-02 5.57e+03 6.94e+00 bond pdb=" N ARG A1469 " pdb=" CA ARG A1469 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.14e-02 7.69e+03 5.95e+00 bond pdb=" N GLU A1465 " pdb=" CA GLU A1465 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.25e-02 6.40e+03 5.12e+00 bond pdb=" N ASP A1467 " pdb=" CA ASP A1467 " ideal model delta sigma weight residual 1.460 1.487 -0.028 1.50e-02 4.44e+03 3.41e+00 ... (remaining 12026 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.63: 329 106.63 - 113.47: 6696 113.47 - 120.31: 4502 120.31 - 127.15: 4630 127.15 - 133.98: 125 Bond angle restraints: 16282 Sorted by residual: angle pdb=" N ARG A1469 " pdb=" CA ARG A1469 " pdb=" C ARG A1469 " ideal model delta sigma weight residual 114.62 106.22 8.40 1.14e+00 7.69e-01 5.43e+01 angle pdb=" CA ARG A1469 " pdb=" C ARG A1469 " pdb=" N ASP A1470 " ideal model delta sigma weight residual 119.71 114.52 5.19 1.17e+00 7.31e-01 1.97e+01 angle pdb=" CA ASP A1467 " pdb=" C ASP A1467 " pdb=" O ASP A1467 " ideal model delta sigma weight residual 121.78 117.58 4.20 1.12e+00 7.97e-01 1.41e+01 angle pdb=" O ARG A1469 " pdb=" C ARG A1469 " pdb=" N ASP A1470 " ideal model delta sigma weight residual 121.67 125.93 -4.26 1.30e+00 5.92e-01 1.07e+01 angle pdb=" CA THR A1466 " pdb=" C THR A1466 " pdb=" O THR A1466 " ideal model delta sigma weight residual 121.87 118.25 3.62 1.16e+00 7.43e-01 9.76e+00 ... (remaining 16277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.76: 7096 33.76 - 67.52: 180 67.52 - 101.28: 23 101.28 - 135.04: 0 135.04 - 168.80: 2 Dihedral angle restraints: 7301 sinusoidal: 3023 harmonic: 4278 Sorted by residual: dihedral pdb=" O4' C C 13 " pdb=" C1' C C 13 " pdb=" N1 C C 13 " pdb=" C2 C C 13 " ideal model delta sinusoidal sigma weight residual 200.00 43.01 156.99 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" O4' U C 14 " pdb=" C1' U C 14 " pdb=" N1 U C 14 " pdb=" C2 U C 14 " ideal model delta sinusoidal sigma weight residual 232.00 63.20 168.80 1 1.70e+01 3.46e-03 6.58e+01 dihedral pdb=" CA LYS A 363 " pdb=" C LYS A 363 " pdb=" N LYS A 364 " pdb=" CA LYS A 364 " ideal model delta harmonic sigma weight residual -180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 7298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1379 0.039 - 0.079: 383 0.079 - 0.118: 85 0.118 - 0.157: 13 0.157 - 0.196: 2 Chirality restraints: 1862 Sorted by residual: chirality pdb=" CB VAL A 133 " pdb=" CA VAL A 133 " pdb=" CG1 VAL A 133 " pdb=" CG2 VAL A 133 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA ILE A 667 " pdb=" N ILE A 667 " pdb=" C ILE A 667 " pdb=" CB ILE A 667 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA ARG A1469 " pdb=" N ARG A1469 " pdb=" C ARG A1469 " pdb=" CB ARG A1469 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1859 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1396 " -0.023 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A1397 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1397 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1397 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 152 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 153 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G C 15 " 0.017 2.00e-02 2.50e+03 8.07e-03 1.95e+00 pdb=" N9 G C 15 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G C 15 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 15 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G C 15 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G C 15 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G C 15 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G C 15 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G C 15 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G C 15 " 0.000 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 338 2.70 - 3.25: 12378 3.25 - 3.80: 19086 3.80 - 4.35: 25075 4.35 - 4.90: 41330 Nonbonded interactions: 98207 Sorted by model distance: nonbonded pdb=" N ASP A1470 " pdb=" OD1 ASP A1470 " model vdw 2.153 2.520 nonbonded pdb=" O GLY A 683 " pdb=" OG SER A 687 " model vdw 2.212 2.440 nonbonded pdb=" O ASP A1490 " pdb=" OG SER A1493 " model vdw 2.231 2.440 nonbonded pdb=" O PRO A1459 " pdb=" NE2 GLN A1483 " model vdw 2.237 2.520 nonbonded pdb=" O SER A1373 " pdb=" OG SER A1376 " model vdw 2.238 2.440 ... (remaining 98202 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 2 6.06 5 P 7 5.49 5 S 80 5.16 5 C 7497 2.51 5 N 1978 2.21 5 O 2226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 4.520 Check model and map are aligned: 0.170 Process input model: 43.920 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12031 Z= 0.196 Angle : 0.566 8.402 16282 Z= 0.318 Chirality : 0.039 0.196 1862 Planarity : 0.003 0.036 2028 Dihedral : 15.253 168.798 4514 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.20), residues: 1428 helix: -0.47 (0.17), residues: 773 sheet: -2.02 (0.49), residues: 91 loop : -3.56 (0.21), residues: 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 1.400 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 24 residues processed: 268 average time/residue: 0.2664 time to fit residues: 100.5199 Evaluate side-chains 186 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.491 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1863 time to fit residues: 8.9767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.0060 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN A 114 GLN A 149 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN A 360 GLN A 508 ASN A 567 ASN A 593 GLN A 607 ASN A 655 HIS A 703 ASN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 ASN A1128 GLN A1132 ASN A1167 ASN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 HIS A1210 GLN ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 ASN ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1443 GLN ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1524 HIS A1530 ASN A1587 GLN A1664 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 12031 Z= 0.203 Angle : 0.617 14.444 16282 Z= 0.305 Chirality : 0.040 0.164 1862 Planarity : 0.004 0.046 2028 Dihedral : 8.469 170.271 1639 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1428 helix: 0.66 (0.18), residues: 783 sheet: -1.87 (0.49), residues: 101 loop : -3.11 (0.24), residues: 544 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 6 residues processed: 196 average time/residue: 0.2719 time to fit residues: 77.1130 Evaluate side-chains 166 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1928 time to fit residues: 3.9235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 HIS ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 HIS ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12031 Z= 0.194 Angle : 0.592 10.940 16282 Z= 0.294 Chirality : 0.040 0.185 1862 Planarity : 0.004 0.046 2028 Dihedral : 8.450 170.805 1639 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 1.43 % 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: -0.89 (0.22), residues: 1428 helix: 1.06 (0.18), residues: 785 sheet: -1.64 (0.51), residues: 99 loop : -2.99 (0.24), residues: 544 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 190 average time/residue: 0.2528 time to fit residues: 70.2660 Evaluate side-chains 164 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.365 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1176 time to fit residues: 3.6851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 131 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 696 ASN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 ASN ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 GLN A1301 ASN ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12031 Z= 0.192 Angle : 0.582 9.148 16282 Z= 0.289 Chirality : 0.039 0.151 1862 Planarity : 0.004 0.044 2028 Dihedral : 8.417 171.293 1639 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 1.28 % 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: -0.62 (0.23), residues: 1428 helix: 1.27 (0.19), residues: 784 sheet: -1.48 (0.51), residues: 101 loop : -2.86 (0.24), residues: 543 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 180 average time/residue: 0.2640 time to fit residues: 68.8322 Evaluate side-chains 162 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1277 time to fit residues: 3.6002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN A 636 GLN ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 12031 Z= 0.230 Angle : 0.604 9.058 16282 Z= 0.301 Chirality : 0.040 0.178 1862 Planarity : 0.004 0.044 2028 Dihedral : 8.439 170.714 1639 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 1.13 % 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: -0.54 (0.23), residues: 1428 helix: 1.29 (0.18), residues: 788 sheet: -1.38 (0.51), residues: 101 loop : -2.80 (0.25), residues: 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 179 average time/residue: 0.2551 time to fit residues: 66.6800 Evaluate side-chains 168 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1251 time to fit residues: 4.3770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 12031 Z= 0.244 Angle : 0.618 10.272 16282 Z= 0.308 Chirality : 0.040 0.189 1862 Planarity : 0.004 0.043 2028 Dihedral : 8.453 170.373 1639 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 0.91 % 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: -0.48 (0.23), residues: 1428 helix: 1.31 (0.18), residues: 788 sheet: -1.21 (0.53), residues: 101 loop : -2.75 (0.25), residues: 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 178 average time/residue: 0.2457 time to fit residues: 64.4479 Evaluate side-chains 164 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1079 time to fit residues: 3.1527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN A 696 ASN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12031 Z= 0.227 Angle : 0.602 9.937 16282 Z= 0.301 Chirality : 0.040 0.239 1862 Planarity : 0.004 0.042 2028 Dihedral : 8.437 170.971 1639 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 0.83 % 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: -0.36 (0.23), residues: 1428 helix: 1.40 (0.18), residues: 782 sheet: -1.34 (0.57), residues: 90 loop : -2.57 (0.25), residues: 556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 172 average time/residue: 0.2454 time to fit residues: 62.4542 Evaluate side-chains 166 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.482 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1075 time to fit residues: 3.5354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12031 Z= 0.243 Angle : 0.629 11.346 16282 Z= 0.312 Chirality : 0.041 0.232 1862 Planarity : 0.004 0.041 2028 Dihedral : 8.438 170.890 1639 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 0.38 % 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: -0.33 (0.23), residues: 1428 helix: 1.41 (0.19), residues: 781 sheet: -1.33 (0.57), residues: 90 loop : -2.53 (0.25), residues: 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.503 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 164 average time/residue: 0.2513 time to fit residues: 60.6199 Evaluate side-chains 158 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.482 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1251 time to fit residues: 2.9217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 0.0270 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 0.0770 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 12031 Z= 0.176 Angle : 0.604 11.821 16282 Z= 0.299 Chirality : 0.040 0.231 1862 Planarity : 0.004 0.042 2028 Dihedral : 8.414 174.573 1639 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1428 helix: 1.48 (0.19), residues: 783 sheet: -1.28 (0.57), residues: 90 loop : -2.47 (0.25), residues: 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.554 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2520 time to fit residues: 65.7697 Evaluate side-chains 161 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 11 optimal weight: 0.0070 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1443 GLN ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 12031 Z= 0.198 Angle : 0.616 11.695 16282 Z= 0.306 Chirality : 0.041 0.382 1862 Planarity : 0.004 0.042 2028 Dihedral : 8.395 174.068 1639 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1428 helix: 1.45 (0.19), residues: 786 sheet: -1.32 (0.56), residues: 90 loop : -2.39 (0.25), residues: 552 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.585 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 163 average time/residue: 0.2505 time to fit residues: 60.4402 Evaluate side-chains 158 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1142 time to fit residues: 2.3108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 0.0670 chunk 47 optimal weight: 0.7980 chunk 117 optimal weight: 0.0470 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 100 optimal weight: 0.2980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.182627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142646 restraints weight = 22197.772| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.96 r_work: 0.3208 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 12031 Z= 0.166 Angle : 0.601 11.671 16282 Z= 0.298 Chirality : 0.040 0.391 1862 Planarity : 0.004 0.042 2028 Dihedral : 8.334 175.022 1639 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1428 helix: 1.52 (0.19), residues: 783 sheet: -1.32 (0.56), residues: 90 loop : -2.32 (0.25), residues: 555 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: