Starting phenix.real_space_refine (version: dev) on Fri Mar 17 19:48:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/03_2023/7jge_22324.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/03_2023/7jge_22324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/03_2023/7jge_22324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/03_2023/7jge_22324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/03_2023/7jge_22324.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/03_2023/7jge_22324.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A ASP 324": "OD1" <-> "OD2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 748": "OD1" <-> "OD2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 805": "OD1" <-> "OD2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 913": "OD1" <-> "OD2" Residue "A TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A ASP 976": "OD1" <-> "OD2" Residue "A GLU 1003": "OE1" <-> "OE2" Residue "A TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1011": "OD1" <-> "OD2" Residue "A TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1047": "OE1" <-> "OE2" Residue "A TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1116": "OD1" <-> "OD2" Residue "A TYR 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1128": "OD1" <-> "OD2" Residue "A PHE 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1151": "OE1" <-> "OE2" Residue "A ASP 1171": "OD1" <-> "OD2" Residue "A PHE 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A GLU 1204": "OE1" <-> "OE2" Residue "A TYR 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1276": "OE1" <-> "OE2" Residue "A GLU 1298": "OE1" <-> "OE2" Residue "A ASP 1316": "OD1" <-> "OD2" Residue "A PHE 1343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1367": "OE1" <-> "OE2" Residue "A ASP 1414": "OD1" <-> "OD2" Residue "A GLU 1436": "OE1" <-> "OE2" Residue "A ASP 1448": "OD1" <-> "OD2" Residue "A PHE 1454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1495": "OD1" <-> "OD2" Residue "A TYR 1511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1514": "OE1" <-> "OE2" Residue "A TYR 1543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1551": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1555": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1561": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1569": "OD1" <-> "OD2" Residue "A TYR 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1582": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1584": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1588": "OE1" <-> "OE2" Residue "A ASP 1602": "OD1" <-> "OD2" Residue "A TYR 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1623": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1652": "OE1" <-> "OE2" Residue "A GLU 1653": "OE1" <-> "OE2" Residue "A TYR 1667": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1696": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1724": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1740": "OD1" <-> "OD2" Residue "A TYR 1770": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1773": "OE1" <-> "OE2" Residue "A GLU 1808": "OE1" <-> "OE2" Residue "A TYR 1810": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1813": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1845": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1863": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1873": "OE1" <-> "OE2" Residue "A GLU 1875": "OE1" <-> "OE2" Residue "A TYR 1880": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 20315 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 20315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1437, 20315 Classifications: {'peptide': 1437} Link IDs: {'PTRANS': 38, 'TRANS': 1398} Chain breaks: 27 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 9.54, per 1000 atoms: 0.47 Number of scatterers: 20315 At special positions: 0 Unit cell: (115.322, 133.308, 136.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 O 2276 8.00 N 2012 7.00 C 7433 6.00 H 8508 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS A 645 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A 771 " - pdb=" SG CYS A 910 " distance=2.03 Simple disulfide: pdb=" SG CYS A 785 " - pdb=" SG CYS A 803 " distance=2.03 Simple disulfide: pdb=" SG CYS A 799 " - pdb=" SG CYS A 966 " distance=2.03 Simple disulfide: pdb=" SG CYS A 807 " - pdb=" SG CYS A 964 " distance=2.03 Simple disulfide: pdb=" SG CYS A 817 " - pdb=" SG CYS A 929 " distance=2.03 Simple disulfide: pdb=" SG CYS A 975 " - pdb=" SG CYS A1099 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS A1005 " distance=2.03 Simple disulfide: pdb=" SG CYS A1097 " - pdb=" SG CYS A1202 " distance=2.03 Simple disulfide: pdb=" SG CYS A1149 " - pdb=" SG CYS A1180 " distance=2.03 Simple disulfide: pdb=" SG CYS A1219 " - pdb=" SG CYS A1418 " distance=2.03 Simple disulfide: pdb=" SG CYS A1230 " - pdb=" SG CYS A1273 " distance=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1264 " distance=2.03 Simple disulfide: pdb=" SG CYS A1344 " - pdb=" SG CYS A1437 " distance=2.03 Simple disulfide: pdb=" SG CYS A1462 " - pdb=" SG CYS A1546 " distance=2.03 Simple disulfide: pdb=" SG CYS A1476 " - pdb=" SG CYS A1501 " distance=2.03 Simple disulfide: pdb=" SG CYS A1505 " - pdb=" SG CYS A1574 " distance=2.03 Simple disulfide: pdb=" SG CYS A1596 " - pdb=" SG CYS A1632 " distance=2.03 Simple disulfide: pdb=" SG CYS A1688 " - pdb=" SG CYS A1782 " distance=2.03 Simple disulfide: pdb=" SG CYS A1689 " - pdb=" SG CYS A1906 " distance=2.03 Simple disulfide: pdb=" SG CYS A1807 " - pdb=" SG CYS A1909 " distance=2.03 Simple disulfide: pdb=" SG CYS A1821 " - pdb=" SG CYS A1838 " distance=2.03 Simple disulfide: pdb=" SG CYS A1842 " - pdb=" SG CYS A1933 " distance=2.03 Simple disulfide: pdb=" SG CYS A1896 " - pdb=" SG CYS A1907 " 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: 15.58 Conformation dependent library (CDL) restraints added in 2.6 seconds 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 1 sheets defined 59.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 99 through 105 removed outlier: 4.084A pdb=" N ARG A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 105 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 143 removed outlier: 3.997A pdb=" N PHE A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.664A pdb=" N ILE A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.586A pdb=" N GLU A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 223 through 229 removed outlier: 4.633A pdb=" N ILE A 226 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR A 227 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 229 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 305 removed outlier: 3.610A pdb=" N GLU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 355 removed outlier: 3.580A pdb=" N LYS A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.654A pdb=" N GLN A 585 " --> pdb=" O PRO A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 617 through 636 removed outlier: 4.422A pdb=" N SER A 621 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Proline residue: A 633 - end of helix Processing helix chain 'A' and resid 642 through 661 removed outlier: 4.213A pdb=" N LYS A 646 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.962A pdb=" N LEU A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 722 removed outlier: 3.575A pdb=" N LEU A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR A 718 " --> pdb=" O THR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 785 removed outlier: 3.518A pdb=" N GLN A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 784 " --> pdb=" O ASP A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 815 Processing helix chain 'A' and resid 830 through 852 removed outlier: 3.663A pdb=" N ARG A 834 " --> pdb=" O PRO A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 893 Processing helix chain 'A' and resid 896 through 905 removed outlier: 3.526A pdb=" N TYR A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 977 Processing helix chain 'A' and resid 1028 through 1052 removed outlier: 3.762A pdb=" N LYS A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN A1043 " --> pdb=" O ASN A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1128 removed outlier: 3.729A pdb=" N ASP A1128 " --> pdb=" O LYS A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1158 removed outlier: 3.771A pdb=" N LYS A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A1157 " --> pdb=" O TYR A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1180 removed outlier: 3.511A pdb=" N PHE A1175 " --> pdb=" O ASP A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1206 removed outlier: 3.876A pdb=" N CYS A1202 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1271 removed outlier: 3.861A pdb=" N GLN A1270 " --> pdb=" O PRO A1266 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN A1271 " --> pdb=" O PRO A1267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1266 through 1271' Processing helix chain 'A' and resid 1296 through 1318 Processing helix chain 'A' and resid 1342 through 1360 removed outlier: 3.931A pdb=" N ALA A1346 " --> pdb=" O GLY A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1380 Processing helix chain 'A' and resid 1403 through 1428 Processing helix chain 'A' and resid 1449 through 1476 Processing helix chain 'A' and resid 1500 through 1530 removed outlier: 3.799A pdb=" N LYS A1504 " --> pdb=" O ALA A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1542 removed outlier: 4.103A pdb=" N LEU A1538 " --> pdb=" O SER A1534 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1555 Processing helix chain 'A' and resid 1570 through 1575 Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 3.808A pdb=" N LEU A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1643 removed outlier: 4.303A pdb=" N ILE A1639 " --> pdb=" O GLU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1674 removed outlier: 5.010A pdb=" N GLU A1652 " --> pdb=" O GLU A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1678 Processing helix chain 'A' and resid 1680 through 1704 Processing helix chain 'A' and resid 1710 through 1724 removed outlier: 4.158A pdb=" N TYR A1715 " --> pdb=" O GLU A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1744 Processing helix chain 'A' and resid 1755 through 1773 Processing helix chain 'A' and resid 1793 through 1821 Processing helix chain 'A' and resid 1837 through 1866 Proline residue: A1851 - end of helix removed outlier: 3.919A pdb=" N ILE A1854 " --> pdb=" O ASN A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1893 removed outlier: 3.511A pdb=" N LEU A1892 " --> pdb=" O VAL A1888 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A1893 " --> pdb=" O ILE A1889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1915 through 1921 removed outlier: 3.974A pdb=" N THR A1921 " --> pdb=" O THR A1917 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1949 removed outlier: 3.783A pdb=" N CYS A1933 " --> pdb=" O LYS A1929 " (cutoff:3.500A) Proline residue: A1939 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 920 through 923 609 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.43 Time building geometry restraints manager: 16.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8495 1.04 - 1.23: 315 1.23 - 1.43: 4835 1.43 - 1.63: 6799 1.63 - 1.82: 103 Bond restraints: 20547 Sorted by residual: bond pdb=" CG PRO A1266 " pdb=" CD PRO A1266 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.12e-01 bond pdb=" CG LEU A 294 " pdb=" CD2 LEU A 294 " ideal model delta sigma weight residual 1.521 1.549 -0.028 3.30e-02 9.18e+02 7.29e-01 bond pdb=" CB PRO A1266 " pdb=" CG PRO A1266 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.06e-01 bond pdb=" CG LEU A 294 " pdb=" CD1 LEU A 294 " ideal model delta sigma weight residual 1.521 1.548 -0.027 3.30e-02 9.18e+02 6.70e-01 bond pdb=" CA VAL A 266 " pdb=" C VAL A 266 " ideal model delta sigma weight residual 1.516 1.524 -0.009 1.11e-02 8.12e+03 5.92e-01 ... (remaining 20542 not shown) Histogram of bond angle deviations from ideal: 73.39 - 85.52: 10 85.52 - 97.64: 0 97.64 - 109.77: 13135 109.77 - 121.89: 18808 121.89 - 134.02: 3705 Bond angle restraints: 35658 Sorted by residual: angle pdb=" CB SER A 832 " pdb=" CA SER A 832 " pdb=" HA SER A 832 " ideal model delta sigma weight residual 109.00 73.39 35.61 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N SER A 832 " pdb=" CA SER A 832 " pdb=" HA SER A 832 " ideal model delta sigma weight residual 110.00 75.90 34.10 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C SER A 832 " pdb=" CA SER A 832 " pdb=" HA SER A 832 " ideal model delta sigma weight residual 109.00 74.99 34.01 3.00e+00 1.11e-01 1.29e+02 angle pdb=" SD MET A 186 " pdb=" CE MET A 186 " pdb=" HE2 MET A 186 " ideal model delta sigma weight residual 109.00 79.19 29.81 3.00e+00 1.11e-01 9.88e+01 angle pdb=" SD MET A 186 " pdb=" CE MET A 186 " pdb=" HE3 MET A 186 " ideal model delta sigma weight residual 109.00 79.25 29.75 3.00e+00 1.11e-01 9.83e+01 ... (remaining 35653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8217 17.94 - 35.87: 581 35.87 - 53.81: 127 53.81 - 71.75: 14 71.75 - 89.68: 7 Dihedral angle restraints: 8946 sinusoidal: 4111 harmonic: 4835 Sorted by residual: dihedral pdb=" CB CYS A 799 " pdb=" SG CYS A 799 " pdb=" SG CYS A 966 " pdb=" CB CYS A 966 " ideal model delta sinusoidal sigma weight residual 93.00 42.49 50.51 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CB CYS A 975 " pdb=" SG CYS A 975 " pdb=" SG CYS A1099 " pdb=" CB CYS A1099 " ideal model delta sinusoidal sigma weight residual 93.00 141.57 -48.57 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CB CYS A1596 " pdb=" SG CYS A1596 " pdb=" SG CYS A1632 " pdb=" CB CYS A1632 " ideal model delta sinusoidal sigma weight residual 93.00 139.78 -46.78 1 1.00e+01 1.00e-02 3.03e+01 ... (remaining 8943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 1665 0.343 - 0.687: 0 0.687 - 1.030: 0 1.030 - 1.373: 0 1.373 - 1.717: 1 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CG LEU A 294 " pdb=" CB LEU A 294 " pdb=" CD1 LEU A 294 " pdb=" CD2 LEU A 294 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.37e+01 chirality pdb=" CA SER A 832 " pdb=" N SER A 832 " pdb=" C SER A 832 " pdb=" CB SER A 832 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA ILE A1250 " pdb=" N ILE A1250 " pdb=" C ILE A1250 " pdb=" CB ILE A1250 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1663 not shown) Planarity restraints: 3150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1265 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A1266 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A1266 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1266 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 756 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO A 757 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 757 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 757 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 665 " -0.008 2.00e-02 2.50e+03 5.31e-03 1.13e+00 pdb=" CG TRP A 665 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 665 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 665 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 665 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 665 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 665 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 665 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 665 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 665 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 665 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 665 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 665 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 665 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 665 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 665 " 0.000 2.00e-02 2.50e+03 ... (remaining 3147 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1351 2.23 - 2.83: 39301 2.83 - 3.42: 46456 3.42 - 4.01: 59943 4.01 - 4.60: 93714 Nonbonded interactions: 240765 Sorted by model distance: nonbonded pdb=" HE1 TRP A1761 " pdb=" O VAL A1785 " model vdw 1.643 1.850 nonbonded pdb="HH22 ARG A1628 " pdb=" OD2 ASP A1706 " model vdw 1.662 1.850 nonbonded pdb=" OE1 GLU A1652 " pdb=" H GLU A1652 " model vdw 1.665 1.850 nonbonded pdb=" OD1 ASP A 234 " pdb=" H LEU A 235 " model vdw 1.711 1.850 nonbonded pdb=" O ILE A1352 " pdb="HD21 ASN A1356 " model vdw 1.717 1.850 ... (remaining 240760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 86 5.16 5 C 7433 2.51 5 N 2012 2.21 5 O 2276 1.98 5 H 8508 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.310 Extract box with map and model: 5.140 Check model and map are aligned: 0.280 Process input model: 56.870 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5373 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 : 0.002 0.042 12039 Z= 0.110 Angle : 0.439 10.499 16167 Z= 0.256 Chirality : 0.053 1.717 1666 Planarity : 0.002 0.042 2068 Dihedral : 13.346 89.684 4569 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1381 helix: 2.90 (0.19), residues: 775 sheet: 1.28 (2.16), residues: 10 loop : -2.48 (0.23), residues: 596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3068 time to fit residues: 58.1867 Evaluate side-chains 110 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.253 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.0000 chunk 129 optimal weight: 0.8980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 845 HIS ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 HIS A1424 ASN ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5601 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 12039 Z= 0.173 Angle : 0.454 10.456 16167 Z= 0.246 Chirality : 0.054 1.708 1666 Planarity : 0.003 0.038 2068 Dihedral : 2.832 21.226 1545 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.61 % 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: 0.81 (0.24), residues: 1381 helix: 2.48 (0.19), residues: 812 sheet: 1.11 (2.00), residues: 10 loop : -2.68 (0.23), residues: 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 131 average time/residue: 0.3605 time to fit residues: 69.0415 Evaluate side-chains 124 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1873 time to fit residues: 4.0571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 35 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN A 845 HIS ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A 955 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 GLN ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN A1857 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5757 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12039 Z= 0.197 Angle : 0.470 10.450 16167 Z= 0.257 Chirality : 0.055 1.722 1666 Planarity : 0.003 0.039 2068 Dihedral : 3.179 21.369 1545 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.31 % 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: 0.65 (0.23), residues: 1381 helix: 2.32 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -2.61 (0.23), residues: 569 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 128 average time/residue: 0.4340 time to fit residues: 82.7141 Evaluate side-chains 120 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2089 time to fit residues: 3.2570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 591 ASN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1027 ASN ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12039 Z= 0.196 Angle : 0.473 10.391 16167 Z= 0.258 Chirality : 0.055 1.721 1666 Planarity : 0.003 0.032 2068 Dihedral : 3.299 18.354 1545 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 0.84 % 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: 0.51 (0.23), residues: 1381 helix: 2.23 (0.18), residues: 821 sheet: None (None), residues: 0 loop : -2.81 (0.22), residues: 560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 139 average time/residue: 0.3624 time to fit residues: 74.8190 Evaluate side-chains 126 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2505 time to fit residues: 5.2370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 2 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 GLN ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1659 GLN A1911 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 12039 Z= 0.330 Angle : 0.600 10.292 16167 Z= 0.337 Chirality : 0.058 1.725 1666 Planarity : 0.004 0.043 2068 Dihedral : 4.048 26.574 1545 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1381 helix: 1.73 (0.18), residues: 821 sheet: -0.50 (2.03), residues: 10 loop : -3.09 (0.22), residues: 550 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 152 average time/residue: 0.4421 time to fit residues: 98.9076 Evaluate side-chains 135 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1935 time to fit residues: 6.0224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 11 optimal weight: 30.0000 chunk 45 optimal weight: 0.0980 chunk 72 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1857 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 12039 Z= 0.180 Angle : 0.481 10.301 16167 Z= 0.263 Chirality : 0.055 1.721 1666 Planarity : 0.003 0.037 2068 Dihedral : 3.641 21.166 1545 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1381 helix: 2.00 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -2.97 (0.22), residues: 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 136 average time/residue: 0.4350 time to fit residues: 86.7773 Evaluate side-chains 126 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2349 time to fit residues: 4.3556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 0.0870 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 12039 Z= 0.360 Angle : 0.622 10.214 16167 Z= 0.351 Chirality : 0.058 1.727 1666 Planarity : 0.004 0.057 2068 Dihedral : 4.244 28.041 1545 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer Outliers : 0.54 % 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: -0.34 (0.23), residues: 1381 helix: 1.54 (0.18), residues: 823 sheet: -0.74 (2.05), residues: 10 loop : -3.21 (0.22), residues: 548 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 141 average time/residue: 0.4401 time to fit residues: 91.9009 Evaluate side-chains 136 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2124 time to fit residues: 4.8704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 40.0000 chunk 26 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1027 ASN ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 12039 Z= 0.276 Angle : 0.550 10.220 16167 Z= 0.304 Chirality : 0.057 1.726 1666 Planarity : 0.004 0.048 2068 Dihedral : 4.090 24.975 1545 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1381 helix: 1.58 (0.18), residues: 823 sheet: None (None), residues: 0 loop : -3.13 (0.22), residues: 558 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 142 average time/residue: 0.4231 time to fit residues: 89.5328 Evaluate side-chains 134 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.705 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2176 time to fit residues: 4.2623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 0.0980 chunk 77 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 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 566 ASN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1674 ASN A1794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 12039 Z= 0.143 Angle : 0.469 10.193 16167 Z= 0.251 Chirality : 0.055 1.722 1666 Planarity : 0.003 0.039 2068 Dihedral : 3.638 19.882 1545 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.23), residues: 1381 helix: 2.00 (0.19), residues: 819 sheet: -0.04 (2.29), residues: 10 loop : -3.08 (0.22), residues: 552 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 131 average time/residue: 0.3842 time to fit residues: 73.9536 Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 294, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 600, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 180, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 132, in run_one_one result.show(prefix=" ") File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 112, in show self.log.flush() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/libtbx/utils.py", line 1570, in flush if (flush is not None): flush() IOError: [Errno 28] No space left on device