Starting phenix.real_space_refine on Thu Feb 15 09:13:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2024/7ela_31178.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2024/7ela_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_2024/7ela_31178.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2024/7ela_31178.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2024/7ela_31178.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ela_31178/02_2024/7ela_31178.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 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. 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-5238/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: 11.86, per 1000 atoms: 1.01 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: 4.48 Conformation dependent library (CDL) restraints added in 3.7 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: 1.58 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: 4.63 Time building geometry restraints manager: 4.90 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: 7108 33.76 - 67.52: 200 67.52 - 101.28: 25 101.28 - 135.04: 0 135.04 - 168.80: 2 Dihedral angle restraints: 7335 sinusoidal: 3057 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 7332 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 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: 0.010 Normalize map: mean=0, sd=1: 0.850 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: 4.020 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 43.810 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 15.708 168.798 4548 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 % Allowed : 8.60 % Favored : 88.60 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1666 HIS 0.006 0.001 HIS A1744 PHE 0.014 0.001 PHE A 541 TYR 0.012 0.001 TYR A 302 ARG 0.002 0.000 ARG A 380 *********************** 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 : 1.324 Fit side-chains revert: symmetry clash REVERT: B 50 CYS cc_start: 0.6258 (p) cc_final: 0.5814 (p) REVERT: B 53 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7744 (m) REVERT: A 343 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7407 (mmtm) REVERT: A 385 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: A 669 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7332 (p0) REVERT: A 751 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7219 (tm-30) REVERT: A 755 MET cc_start: 0.8687 (tpp) cc_final: 0.8429 (tpp) REVERT: A 1223 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.5590 (tp) REVERT: A 1366 ASP cc_start: 0.8442 (t70) cc_final: 0.7816 (t0) REVERT: A 1467 ASP cc_start: 0.6909 (p0) cc_final: 0.6512 (p0) REVERT: A 1469 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6386 (tpm170) REVERT: A 1546 GLU cc_start: 0.7048 (pt0) cc_final: 0.6848 (pt0) REVERT: A 1579 ILE cc_start: 0.3825 (OUTLIER) cc_final: 0.3028 (tp) REVERT: A 1810 TYR cc_start: 0.8148 (m-80) cc_final: 0.7740 (m-80) outliers start: 37 outliers final: 24 residues processed: 268 average time/residue: 0.2642 time to fit residues: 99.1476 Evaluate side-chains 194 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1469 ARG Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1639 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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** 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1289 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= 0.205 Angle : 0.607 14.437 16282 Z= 0.300 Chirality : 0.039 0.165 1862 Planarity : 0.004 0.046 2028 Dihedral : 11.909 169.899 1737 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.55 % Allowed : 12.60 % Favored : 83.85 % 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: -1.30 (0.22), residues: 1428 helix: 0.64 (0.18), residues: 790 sheet: -1.51 (0.52), residues: 89 loop : -3.12 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 394 HIS 0.003 0.001 HIS A1361 PHE 0.012 0.001 PHE A 541 TYR 0.024 0.001 TYR A1125 ARG 0.005 0.000 ARG B 63 *********************** 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 229 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 182 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 CYS cc_start: 0.6889 (p) cc_final: 0.6430 (p) REVERT: B 53 CYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7671 (m) REVERT: A 113 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6534 (mm-30) REVERT: A 276 ASP cc_start: 0.6632 (m-30) cc_final: 0.6425 (m-30) REVERT: A 343 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7422 (mmtm) REVERT: A 384 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8607 (tt) REVERT: A 540 GLU cc_start: 0.6415 (mt-10) cc_final: 0.6156 (mm-30) REVERT: A 647 MET cc_start: 0.8493 (tpt) cc_final: 0.8114 (tpt) REVERT: A 669 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7294 (p0) REVERT: A 751 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7282 (tm-30) REVERT: A 1150 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 1294 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7491 (ttt) REVERT: A 1366 ASP cc_start: 0.8396 (t70) cc_final: 0.7829 (t0) REVERT: A 1467 ASP cc_start: 0.7173 (p0) cc_final: 0.6884 (p0) REVERT: A 1531 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7805 (tp) REVERT: A 1654 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7711 (mm) REVERT: A 1810 TYR cc_start: 0.8227 (m-80) cc_final: 0.7779 (m-80) outliers start: 47 outliers final: 25 residues processed: 214 average time/residue: 0.2685 time to fit residues: 81.6719 Evaluate side-chains 191 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1150 GLU Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 89 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.0060 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 0.0270 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.3254 ------------------------------------------------------------------------------- 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 149 ASN ** 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** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 HIS ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 GLN ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1530 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12031 Z= 0.164 Angle : 0.576 11.728 16282 Z= 0.284 Chirality : 0.039 0.146 1862 Planarity : 0.004 0.051 2028 Dihedral : 11.490 171.684 1719 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.40 % Allowed : 14.34 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1428 helix: 1.10 (0.19), residues: 784 sheet: -1.36 (0.53), residues: 89 loop : -3.01 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1688 HIS 0.015 0.001 HIS A 213 PHE 0.013 0.001 PHE A 541 TYR 0.017 0.001 TYR A1125 ARG 0.004 0.000 ARG A 397 *********************** 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 226 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 CYS cc_start: 0.6789 (p) cc_final: 0.6358 (p) REVERT: A 113 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6592 (mm-30) REVERT: A 384 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8770 (tt) REVERT: A 540 GLU cc_start: 0.6477 (mt-10) cc_final: 0.6200 (mm-30) REVERT: A 622 MET cc_start: 0.8681 (mtm) cc_final: 0.8457 (mtm) REVERT: A 647 MET cc_start: 0.8469 (tpt) cc_final: 0.8110 (tpt) REVERT: A 669 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7228 (p0) REVERT: A 1191 MET cc_start: 0.7385 (mtp) cc_final: 0.7129 (mtp) REVERT: A 1253 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7822 (mtmm) REVERT: A 1366 ASP cc_start: 0.8302 (t70) cc_final: 0.7718 (t0) REVERT: A 1467 ASP cc_start: 0.7108 (p0) cc_final: 0.6808 (p0) REVERT: A 1654 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7536 (mm) REVERT: A 1701 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7882 (pp) REVERT: A 1810 TYR cc_start: 0.8187 (m-80) cc_final: 0.7695 (m-80) outliers start: 45 outliers final: 28 residues processed: 215 average time/residue: 0.2460 time to fit residues: 75.7521 Evaluate side-chains 194 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 149 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1530 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12031 Z= 0.316 Angle : 0.632 12.510 16282 Z= 0.314 Chirality : 0.041 0.174 1862 Planarity : 0.004 0.049 2028 Dihedral : 11.472 169.091 1716 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.85 % Allowed : 15.62 % Favored : 80.53 % 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: -0.74 (0.22), residues: 1428 helix: 1.10 (0.18), residues: 788 sheet: -1.21 (0.54), residues: 89 loop : -2.87 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 369 HIS 0.005 0.001 HIS A 213 PHE 0.016 0.002 PHE A 258 TYR 0.016 0.002 TYR A1125 ARG 0.004 0.001 ARG A 663 *********************** 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 219 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 168 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 CYS cc_start: 0.7322 (p) cc_final: 0.7117 (p) REVERT: A 40 MET cc_start: 0.5440 (tmm) cc_final: 0.5193 (tmm) REVERT: A 540 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6204 (mm-30) REVERT: A 647 MET cc_start: 0.8679 (tpt) cc_final: 0.8000 (tpt) REVERT: A 669 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7407 (p0) REVERT: A 1253 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7815 (mtmm) REVERT: A 1311 GLU cc_start: 0.7756 (tp30) cc_final: 0.7070 (tp30) REVERT: A 1366 ASP cc_start: 0.8381 (t70) cc_final: 0.7812 (t0) REVERT: A 1467 ASP cc_start: 0.7221 (p0) cc_final: 0.6989 (p0) REVERT: A 1531 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7493 (tp) REVERT: A 1579 ILE cc_start: 0.3989 (OUTLIER) cc_final: 0.3213 (tp) REVERT: A 1810 TYR cc_start: 0.8218 (m-80) cc_final: 0.7761 (m-80) outliers start: 51 outliers final: 36 residues processed: 207 average time/residue: 0.2446 time to fit residues: 72.6878 Evaluate side-chains 202 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 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 399 GLN ** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 GLN A1301 ASN ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12031 Z= 0.220 Angle : 0.588 12.030 16282 Z= 0.292 Chirality : 0.039 0.164 1862 Planarity : 0.004 0.049 2028 Dihedral : 11.330 170.501 1713 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.62 % Allowed : 15.77 % Favored : 80.60 % 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: -0.57 (0.23), residues: 1428 helix: 1.25 (0.18), residues: 787 sheet: -1.23 (0.55), residues: 89 loop : -2.78 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 394 HIS 0.005 0.001 HIS A 213 PHE 0.012 0.001 PHE A 258 TYR 0.016 0.001 TYR A1125 ARG 0.004 0.000 ARG A 397 *********************** 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 222 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 174 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 TYR cc_start: 0.7696 (m-80) cc_final: 0.7487 (m-10) REVERT: B 50 CYS cc_start: 0.7011 (p) cc_final: 0.6610 (p) REVERT: A 40 MET cc_start: 0.5566 (tmm) cc_final: 0.5264 (tmm) REVERT: A 388 LYS cc_start: 0.8340 (mtpt) cc_final: 0.8134 (mtmm) REVERT: A 540 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6174 (mm-30) REVERT: A 622 MET cc_start: 0.8678 (mtm) cc_final: 0.8440 (mtm) REVERT: A 647 MET cc_start: 0.8648 (tpt) cc_final: 0.8021 (tpt) REVERT: A 669 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7322 (p0) REVERT: A 1191 MET cc_start: 0.7451 (mtp) cc_final: 0.7205 (mtp) REVERT: A 1253 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7791 (mtmm) REVERT: A 1366 ASP cc_start: 0.8299 (t70) cc_final: 0.7744 (t0) REVERT: A 1467 ASP cc_start: 0.7206 (p0) cc_final: 0.6960 (p0) REVERT: A 1579 ILE cc_start: 0.4027 (OUTLIER) cc_final: 0.3537 (tt) REVERT: A 1810 TYR cc_start: 0.8207 (m-80) cc_final: 0.7764 (m-80) outliers start: 48 outliers final: 36 residues processed: 209 average time/residue: 0.2485 time to fit residues: 74.3956 Evaluate side-chains 202 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.0010 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 149 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12031 Z= 0.199 Angle : 0.584 13.034 16282 Z= 0.290 Chirality : 0.039 0.180 1862 Planarity : 0.004 0.046 2028 Dihedral : 11.251 172.006 1713 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.77 % Allowed : 16.45 % Favored : 79.77 % 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: -0.41 (0.23), residues: 1428 helix: 1.42 (0.19), residues: 781 sheet: -1.45 (0.55), residues: 80 loop : -2.67 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 394 HIS 0.004 0.001 HIS A 213 PHE 0.012 0.001 PHE A 799 TYR 0.016 0.001 TYR A1125 ARG 0.004 0.000 ARG A 397 *********************** 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 227 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 177 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7400 (pp30) REVERT: A 420 ASN cc_start: 0.7808 (t0) cc_final: 0.7555 (t0) REVERT: A 540 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6226 (mm-30) REVERT: A 622 MET cc_start: 0.8688 (mtm) cc_final: 0.8474 (mtm) REVERT: A 647 MET cc_start: 0.8647 (tpt) cc_final: 0.8019 (tpt) REVERT: A 669 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7281 (p0) REVERT: A 1191 MET cc_start: 0.7454 (mtp) cc_final: 0.7209 (mtp) REVERT: A 1253 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7795 (mtmm) REVERT: A 1366 ASP cc_start: 0.8227 (t70) cc_final: 0.7685 (t0) REVERT: A 1467 ASP cc_start: 0.7228 (p0) cc_final: 0.6896 (p0) REVERT: A 1579 ILE cc_start: 0.4033 (OUTLIER) cc_final: 0.3634 (tt) REVERT: A 1810 TYR cc_start: 0.8163 (m-80) cc_final: 0.7754 (m-80) outliers start: 50 outliers final: 38 residues processed: 215 average time/residue: 0.2456 time to fit residues: 75.8309 Evaluate side-chains 207 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 166 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 399 GLN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12031 Z= 0.208 Angle : 0.592 11.865 16282 Z= 0.293 Chirality : 0.040 0.248 1862 Planarity : 0.004 0.044 2028 Dihedral : 11.229 172.062 1713 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.55 % Allowed : 17.43 % Favored : 79.02 % 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: -0.35 (0.23), residues: 1428 helix: 1.45 (0.19), residues: 782 sheet: -1.27 (0.57), residues: 80 loop : -2.64 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 394 HIS 0.004 0.001 HIS A 213 PHE 0.036 0.001 PHE A 104 TYR 0.016 0.001 TYR A1125 ARG 0.002 0.000 ARG A 362 *********************** 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 223 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 176 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 TYR cc_start: 0.7698 (m-80) cc_final: 0.7491 (m-10) REVERT: A 40 MET cc_start: 0.5370 (tmm) cc_final: 0.5162 (tmm) REVERT: A 360 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7447 (pp30) REVERT: A 420 ASN cc_start: 0.7816 (t0) cc_final: 0.7557 (t0) REVERT: A 540 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6211 (mm-30) REVERT: A 647 MET cc_start: 0.8652 (tpt) cc_final: 0.8002 (tpt) REVERT: A 669 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7286 (p0) REVERT: A 1191 MET cc_start: 0.7463 (mtp) cc_final: 0.7215 (mtp) REVERT: A 1253 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7796 (mtmm) REVERT: A 1366 ASP cc_start: 0.8218 (t70) cc_final: 0.7674 (t0) REVERT: A 1467 ASP cc_start: 0.7316 (p0) cc_final: 0.7001 (p0) REVERT: A 1579 ILE cc_start: 0.3930 (OUTLIER) cc_final: 0.3545 (tt) REVERT: A 1810 TYR cc_start: 0.8160 (m-80) cc_final: 0.7748 (m-80) outliers start: 47 outliers final: 40 residues processed: 212 average time/residue: 0.2475 time to fit residues: 75.1112 Evaluate side-chains 210 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 12 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 149 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 696 ASN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 ASN ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12031 Z= 0.249 Angle : 0.607 10.834 16282 Z= 0.302 Chirality : 0.041 0.239 1862 Planarity : 0.004 0.044 2028 Dihedral : 11.239 172.388 1713 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.62 % Allowed : 17.36 % Favored : 79.02 % 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: -0.37 (0.23), residues: 1428 helix: 1.42 (0.19), residues: 782 sheet: -1.28 (0.56), residues: 80 loop : -2.63 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 394 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.001 PHE A 258 TYR 0.016 0.001 TYR A1125 ARG 0.004 0.000 ARG A 362 *********************** 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 216 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 168 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.6934 (t) REVERT: A 40 MET cc_start: 0.5431 (tmm) cc_final: 0.5214 (tmm) REVERT: A 360 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7728 (pp30) REVERT: A 420 ASN cc_start: 0.7826 (t0) cc_final: 0.7568 (t0) REVERT: A 622 MET cc_start: 0.8658 (mtm) cc_final: 0.8370 (mtm) REVERT: A 647 MET cc_start: 0.8668 (tpt) cc_final: 0.7931 (tpt) REVERT: A 669 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7380 (p0) REVERT: A 1191 MET cc_start: 0.7497 (mtp) cc_final: 0.7249 (mtp) REVERT: A 1253 LYS cc_start: 0.8004 (mmmt) cc_final: 0.7785 (mtmm) REVERT: A 1366 ASP cc_start: 0.8251 (t70) cc_final: 0.7707 (t0) REVERT: A 1579 ILE cc_start: 0.3944 (OUTLIER) cc_final: 0.3558 (tt) REVERT: A 1810 TYR cc_start: 0.8208 (m-80) cc_final: 0.7793 (m-80) outliers start: 48 outliers final: 41 residues processed: 204 average time/residue: 0.2498 time to fit residues: 73.2654 Evaluate side-chains 211 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 664 GLU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1400 THR Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1458 ASP Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 129 optimal weight: 0.0570 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 0.0070 chunk 101 optimal weight: 0.0470 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 overall best weight: 0.2614 ------------------------------------------------------------------------------- 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 149 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN A 360 GLN A 636 GLN ** A1238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12031 Z= 0.156 Angle : 0.586 11.369 16282 Z= 0.289 Chirality : 0.039 0.240 1862 Planarity : 0.004 0.042 2028 Dihedral : 11.181 175.087 1713 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.17 % Allowed : 17.74 % Favored : 79.09 % 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: -0.18 (0.23), residues: 1428 helix: 1.57 (0.19), residues: 785 sheet: -1.21 (0.58), residues: 78 loop : -2.54 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 394 HIS 0.007 0.001 HIS A 358 PHE 0.009 0.001 PHE A 799 TYR 0.017 0.001 TYR A1125 ARG 0.004 0.000 ARG A 362 *********************** 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 225 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.5427 (tmm) cc_final: 0.5206 (tmm) REVERT: A 360 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7697 (pp30) REVERT: A 420 ASN cc_start: 0.7782 (t0) cc_final: 0.7507 (t0) REVERT: A 547 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6963 (mt-10) REVERT: A 622 MET cc_start: 0.8615 (mtm) cc_final: 0.8352 (mtm) REVERT: A 640 GLN cc_start: 0.7724 (mt0) cc_final: 0.7499 (mt0) REVERT: A 647 MET cc_start: 0.8592 (tpt) cc_final: 0.8004 (tpt) REVERT: A 669 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7294 (p0) REVERT: A 1191 MET cc_start: 0.7352 (mtp) cc_final: 0.7129 (mtp) REVERT: A 1223 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.5988 (mm) REVERT: A 1253 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7757 (mtmm) REVERT: A 1290 SER cc_start: 0.8079 (t) cc_final: 0.7709 (m) REVERT: A 1366 ASP cc_start: 0.8120 (t70) cc_final: 0.7855 (t70) REVERT: A 1579 ILE cc_start: 0.3889 (OUTLIER) cc_final: 0.3597 (tt) REVERT: A 1810 TYR cc_start: 0.8119 (m-80) cc_final: 0.7750 (m-80) outliers start: 42 outliers final: 32 residues processed: 217 average time/residue: 0.2943 time to fit residues: 92.8561 Evaluate side-chains 207 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 171 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 132 optimal weight: 0.0980 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 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 360 GLN ** 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** ** A1483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12031 Z= 0.239 Angle : 0.616 11.116 16282 Z= 0.303 Chirality : 0.041 0.230 1862 Planarity : 0.004 0.043 2028 Dihedral : 11.167 173.155 1712 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.79 % Allowed : 18.19 % Favored : 79.02 % 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: 1.49 (0.19), residues: 785 sheet: -1.11 (0.57), residues: 80 loop : -2.52 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 394 HIS 0.007 0.001 HIS A 358 PHE 0.013 0.001 PHE A 258 TYR 0.016 0.001 TYR A1125 ARG 0.006 0.000 ARG A 362 ********************** 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 208 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.5477 (tmm) cc_final: 0.5246 (tmm) REVERT: A 420 ASN cc_start: 0.7822 (t0) cc_final: 0.7565 (t0) REVERT: A 622 MET cc_start: 0.8665 (mtm) cc_final: 0.8418 (mtm) REVERT: A 640 GLN cc_start: 0.7950 (mt0) cc_final: 0.7625 (mt0) REVERT: A 647 MET cc_start: 0.8673 (tpt) cc_final: 0.7945 (tpt) REVERT: A 669 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7400 (p0) REVERT: A 1191 MET cc_start: 0.7511 (mtp) cc_final: 0.7275 (mtp) REVERT: A 1223 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6129 (mm) REVERT: A 1253 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7781 (mtmm) REVERT: A 1311 GLU cc_start: 0.7699 (tp30) cc_final: 0.7026 (tp30) REVERT: A 1366 ASP cc_start: 0.8193 (t70) cc_final: 0.7652 (t0) REVERT: A 1579 ILE cc_start: 0.4000 (OUTLIER) cc_final: 0.3694 (tt) REVERT: A 1810 TYR cc_start: 0.8178 (m-80) cc_final: 0.7758 (m-80) outliers start: 37 outliers final: 33 residues processed: 199 average time/residue: 0.2628 time to fit residues: 74.4859 Evaluate side-chains 201 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1302 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 THR Chi-restraints excluded: chain A residue 1454 ARG Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1470 ASP Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1531 LEU Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1654 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1801 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 117 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 360 GLN A 636 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.179718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139702 restraints weight = 22114.875| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 4.50 r_work: 0.3152 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12031 Z= 0.185 Angle : 0.593 11.692 16282 Z= 0.293 Chirality : 0.040 0.225 1862 Planarity : 0.004 0.044 2028 Dihedral : 11.116 173.765 1712 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.94 % Allowed : 18.42 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1428 helix: 1.54 (0.19), residues: 785 sheet: -1.10 (0.58), residues: 78 loop : -2.52 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 394 HIS 0.006 0.001 HIS A1186 PHE 0.011 0.001 PHE A1274 TYR 0.016 0.001 TYR A1125 ARG 0.002 0.000 ARG A1141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.14 seconds wall clock time: 52 minutes 33.41 seconds (3153.41 seconds total)