Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 17:35:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/04_2023/7niu_12365_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/04_2023/7niu_12365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/04_2023/7niu_12365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/04_2023/7niu_12365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/04_2023/7niu_12365_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/04_2023/7niu_12365_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 9889 2.51 5 N 2601 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A ARG 1232": "NH1" <-> "NH2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "E GLU 9": "OE1" <-> "OE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ARG 101": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15495 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8780 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 27, 'TRANS': 1105} Chain breaks: 2 Chain: "D" Number of atoms: 1584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 208, 1578 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197} Conformer: "B" Number of residues, atoms: 208, 1575 Classifications: {'peptide': 208} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 197} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1598 Chain: "E" Number of atoms: 1702 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 229, 1702 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217} Chain: "B" Number of atoms: 1616 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1610 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Conformer: "B" Number of residues, atoms: 211, 1607 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1631 Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 234, 1757 Classifications: {'peptide': 234} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.00, per 1000 atoms: 0.65 Number of scatterers: 15495 At special positions: 0 Unit cell: (158.4, 132, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 2952 8.00 N 2601 7.00 C 9889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.02 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 99 " distance=2.02 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 216 " 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: 6.70 Conformation dependent library (CDL) restraints added in 2.8 seconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 25 sheets defined 35.0% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 51 through 91 removed outlier: 4.781A pdb=" N LEU A 71 " --> pdb=" O HIS A 67 " (cutoff:3.500A) Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 109 through 159 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 191 through 212 removed outlier: 3.631A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 268 Proline residue: A 225 - end of helix removed outlier: 5.029A pdb=" N LYS A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 325 removed outlier: 3.728A pdb=" N ILE A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 340 removed outlier: 3.639A pdb=" N ILE A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 351 through 371 removed outlier: 4.239A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 465 through 471 removed outlier: 4.292A pdb=" N GLU A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 removed outlier: 4.468A pdb=" N GLY A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 removed outlier: 4.014A pdb=" N ALA A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 549 removed outlier: 3.542A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 573 Processing helix chain 'A' and resid 614 through 617 No H-bonds generated for 'chain 'A' and resid 614 through 617' Processing helix chain 'A' and resid 624 through 627 No H-bonds generated for 'chain 'A' and resid 624 through 627' Processing helix chain 'A' and resid 697 through 703 Processing helix chain 'A' and resid 708 through 741 removed outlier: 4.903A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 3.507A pdb=" N ALA A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) Proline residue: A 741 - end of helix Processing helix chain 'A' and resid 746 through 749 No H-bonds generated for 'chain 'A' and resid 746 through 749' Processing helix chain 'A' and resid 751 through 797 Processing helix chain 'A' and resid 800 through 802 No H-bonds generated for 'chain 'A' and resid 800 through 802' Processing helix chain 'A' and resid 810 through 852 removed outlier: 3.743A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR A 828 " --> pdb=" O VAL A 824 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 830 " --> pdb=" O GLY A 826 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 863 through 908 removed outlier: 3.549A pdb=" N ALA A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG A 904 " --> pdb=" O ILE A 900 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 908 " --> pdb=" O ARG A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 965 removed outlier: 4.480A pdb=" N GLY A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 3.603A pdb=" N TYR A 961 " --> pdb=" O ARG A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 986 removed outlier: 4.397A pdb=" N VAL A 985 " --> pdb=" O VAL A 981 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALA A 986 " --> pdb=" O PHE A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1012 Processing helix chain 'A' and resid 1079 through 1081 No H-bonds generated for 'chain 'A' and resid 1079 through 1081' Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1105 through 1111 Processing helix chain 'A' and resid 1126 through 1133 removed outlier: 3.818A pdb=" N ILE A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1150 removed outlier: 3.912A pdb=" N SER A1146 " --> pdb=" O ASP A1142 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1157 No H-bonds generated for 'chain 'A' and resid 1154 through 1157' Processing helix chain 'A' and resid 1169 through 1172 No H-bonds generated for 'chain 'A' and resid 1169 through 1172' Processing helix chain 'A' and resid 1177 through 1182 Processing helix chain 'A' and resid 1184 through 1187 Processing helix chain 'A' and resid 1189 through 1191 No H-bonds generated for 'chain 'A' and resid 1189 through 1191' Processing helix chain 'A' and resid 1207 through 1218 removed outlier: 3.688A pdb=" N LYS A1211 " --> pdb=" O THR A1207 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL A1212 " --> pdb=" O GLU A1208 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A1213 " --> pdb=" O SER A1209 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 No H-bonds generated for 'chain 'D' and resid 123 through 126' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'B' and resid 184 through 187 No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing sheet with id= A, first strand: chain 'A' and resid 395 through 397 removed outlier: 3.641A pdb=" N GLU A 395 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN A 454 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 472 through 475 removed outlier: 6.339A pdb=" N ILE A 553 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 475 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 555 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 585 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1034 through 1036 removed outlier: 3.538A pdb=" N THR A1035 " --> pdb=" O LEU A1094 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1094 " --> pdb=" O THR A1035 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1065 through 1067 removed outlier: 5.425A pdb=" N LEU A1241 " --> pdb=" O ALA A1066 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 1113 through 1115 removed outlier: 3.602A pdb=" N VAL A1115 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP A1199 " --> pdb=" O VAL A1115 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 400 through 402 removed outlier: 3.860A pdb=" N LEU A 412 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 20 through 25 Processing sheet with id= H, first strand: chain 'D' and resid 34 through 39 Processing sheet with id= I, first strand: chain 'D' and resid 115 through 119 removed outlier: 5.411A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 146 through 151 Processing sheet with id= K, first strand: chain 'E' and resid 21 through 25 removed outlier: 3.823A pdb=" N ALA E 82 " --> pdb=" O CYS E 25 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 133 through 137 removed outlier: 3.674A pdb=" N GLY E 152 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 164 through 167 removed outlier: 4.007A pdb=" N TYR E 207 " --> pdb=" O VAL E 224 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 176 through 178 Processing sheet with id= O, first strand: chain 'E' and resid 38 through 42 removed outlier: 3.962A pdb=" N TRP E 39 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA E 52 " --> pdb=" O TRP E 39 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ARG E 41 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRP E 50 " --> pdb=" O ARG E 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'B' and resid 20 through 23 Processing sheet with id= Q, first strand: chain 'B' and resid 36 through 39 Processing sheet with id= R, first strand: chain 'B' and resid 90 through 93 Processing sheet with id= S, first strand: chain 'B' and resid 115 through 119 removed outlier: 3.808A pdb=" N GLN B 161 " --> pdb=" O THR B 179 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.594A pdb=" N PHE B 210 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 197 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 206 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.764A pdb=" N SER C 24 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 96 through 101 removed outlier: 3.849A pdb=" N ALA C 100 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'C' and resid 140 through 142 removed outlier: 5.928A pdb=" N TYR C 196 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 170 through 174 630 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.83 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2514 1.28 - 1.42: 4127 1.42 - 1.55: 9084 1.55 - 1.69: 17 1.69 - 1.82: 79 Bond restraints: 15821 Sorted by residual: bond pdb=" C LEU A1217 " pdb=" O LEU A1217 " ideal model delta sigma weight residual 1.235 1.150 0.084 1.40e-02 5.10e+03 3.62e+01 bond pdb=" N GLU A1023 " pdb=" CA GLU A1023 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.22e-02 6.72e+03 7.87e+00 bond pdb=" N ILE A 342 " pdb=" CA ILE A 342 " ideal model delta sigma weight residual 1.463 1.495 -0.032 1.14e-02 7.69e+03 7.70e+00 bond pdb=" N VAL A 985 " pdb=" CA VAL A 985 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.68e+00 bond pdb=" N ILE A1017 " pdb=" CA ILE A1017 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.23e-02 6.61e+03 7.25e+00 ... (remaining 15816 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.80: 234 104.80 - 112.12: 7894 112.12 - 119.44: 5267 119.44 - 126.76: 7886 126.76 - 134.08: 177 Bond angle restraints: 21458 Sorted by residual: angle pdb=" N VAL A 746 " pdb=" CA VAL A 746 " pdb=" C VAL A 746 " ideal model delta sigma weight residual 110.36 120.49 -10.13 1.05e+00 9.07e-01 9.30e+01 angle pdb=" C TRP A 214 " pdb=" N LYS A 215 " pdb=" CA LYS A 215 " ideal model delta sigma weight residual 122.17 114.16 8.01 1.54e+00 4.22e-01 2.70e+01 angle pdb=" N ILE A1236 " pdb=" CA ILE A1236 " pdb=" C ILE A1236 " ideal model delta sigma weight residual 111.90 107.98 3.92 8.10e-01 1.52e+00 2.35e+01 angle pdb=" N ILE A1153 " pdb=" CA ILE A1153 " pdb=" C ILE A1153 " ideal model delta sigma weight residual 113.71 109.44 4.27 9.50e-01 1.11e+00 2.02e+01 angle pdb=" N ASP A1218 " pdb=" CA ASP A1218 " pdb=" C ASP A1218 " ideal model delta sigma weight residual 110.80 119.97 -9.17 2.13e+00 2.20e-01 1.85e+01 ... (remaining 21453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8237 17.87 - 35.74: 942 35.74 - 53.62: 185 53.62 - 71.49: 40 71.49 - 89.36: 15 Dihedral angle restraints: 9419 sinusoidal: 3601 harmonic: 5818 Sorted by residual: dihedral pdb=" CB CYS D 24 " pdb=" SG CYS D 24 " pdb=" SG CYS D 89 " pdb=" CB CYS D 89 " ideal model delta sinusoidal sigma weight residual 93.00 160.17 -67.17 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CA VAL A 964 " pdb=" C VAL A 964 " pdb=" N ASN A 965 " pdb=" CA ASN A 965 " ideal model delta harmonic sigma weight residual 180.00 152.18 27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ALA D 85 " pdb=" C ALA D 85 " pdb=" N THR D 86 " pdb=" CA THR D 86 " ideal model delta harmonic sigma weight residual 180.00 152.42 27.58 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 9416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1893 0.062 - 0.123: 476 0.123 - 0.185: 70 0.185 - 0.247: 8 0.247 - 0.309: 4 Chirality restraints: 2451 Sorted by residual: chirality pdb=" CA TYR A 328 " pdb=" N TYR A 328 " pdb=" C TYR A 328 " pdb=" CB TYR A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C14 CLR A1301 " pdb=" C13 CLR A1301 " pdb=" C15 CLR A1301 " pdb=" C8 CLR A1301 " both_signs ideal model delta sigma weight residual False -2.32 -2.60 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C17 CLR A1302 " pdb=" C13 CLR A1302 " pdb=" C16 CLR A1302 " pdb=" C20 CLR A1302 " both_signs ideal model delta sigma weight residual False 2.55 2.82 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2448 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 305 " -0.027 2.00e-02 2.50e+03 2.28e-02 9.08e+00 pdb=" CG PHE A 305 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 305 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 305 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 305 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 305 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 305 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 154 " -0.008 2.00e-02 2.50e+03 1.83e-02 5.83e+00 pdb=" CG PHE A 154 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 154 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 154 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 154 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 154 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 154 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 827 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C ALA A 827 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA A 827 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 828 " -0.012 2.00e-02 2.50e+03 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 625 2.67 - 3.23: 16535 3.23 - 3.78: 24404 3.78 - 4.34: 32883 4.34 - 4.90: 51760 Nonbonded interactions: 126207 Sorted by model distance: nonbonded pdb=" N GLU A1023 " pdb=" OE1 GLU A1023 " model vdw 2.110 2.520 nonbonded pdb=" OG1 THR A 706 " pdb=" OE1 GLU A 707 " model vdw 2.175 2.440 nonbonded pdb=" OG1 THR A 857 " pdb=" N LEU A 858 " model vdw 2.198 2.520 nonbonded pdb=" O ALA A 840 " pdb=" OG1 THR A 844 " model vdw 2.199 2.440 nonbonded pdb=" OE2 GLU A 275 " pdb=" NH1 ARG A 278 " model vdw 2.199 2.520 ... (remaining 126202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 91 or resid 94 or resid 96 through 114 or resid \ 116 through 156 or resid 158 through 203 or resid 205 through 213)) selection = (chain 'D' and (resid 6 through 91 or resid 94 or resid 96 through 114 or resid \ 116 through 156 or resid 158 through 203 or resid 205 through 213)) } ncs_group { reference = (chain 'C' and (resid 3 through 31 or resid 34 through 35 or resid 37 through 52 \ or resid 54 through 56 or resid 59 through 101 or resid 109 or resid 111 throug \ h 112 or resid 115 or resid 121 through 236)) selection = (chain 'E' and (resid 3 through 31 or resid 34 through 35 or resid 37 through 52 \ or resid 54 through 56 or resid 59 through 101 or resid 103 or resid 105 throug \ h 106 or resid 108 or resid 114 through 229)) } 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=0.30 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: 4.930 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: 0.030 Extract box with map and model: 19.950 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 44.810 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 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 : 0.008 0.084 15821 Z= 0.514 Angle : 1.014 11.321 21458 Z= 0.575 Chirality : 0.055 0.309 2451 Planarity : 0.006 0.050 2716 Dihedral : 15.899 89.361 5671 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 34.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.74 % Favored : 85.01 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -5.18 (0.14), residues: 2005 helix: -3.56 (0.13), residues: 682 sheet: -2.80 (0.23), residues: 368 loop : -3.58 (0.16), residues: 955 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 211 average time/residue: 0.3341 time to fit residues: 99.8202 Evaluate side-chains 131 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2110 time to fit residues: 6.7622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 40.0000 chunk 150 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN A 332 ASN ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS A 748 GLN A 749 GLN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN A1231 HIS D 7 GLN D 91 GLN E 184 GLN B 28 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 161 GLN B 167 GLN B 211 ASN C 31 ASN C 87 ASN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5621 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 15821 Z= 0.254 Angle : 0.707 14.011 21458 Z= 0.371 Chirality : 0.046 0.233 2451 Planarity : 0.005 0.051 2716 Dihedral : 6.749 103.592 2188 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -3.75 (0.16), residues: 2005 helix: -1.87 (0.17), residues: 675 sheet: -2.42 (0.23), residues: 396 loop : -2.95 (0.18), residues: 934 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 186 average time/residue: 0.3097 time to fit residues: 86.9323 Evaluate side-chains 129 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.747 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 150 optimal weight: 0.0170 chunk 123 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 145 optimal weight: 30.0000 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15821 Z= 0.205 Angle : 0.648 10.827 21458 Z= 0.338 Chirality : 0.044 0.225 2451 Planarity : 0.004 0.050 2716 Dihedral : 6.190 103.637 2188 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -2.83 (0.17), residues: 2005 helix: -0.89 (0.19), residues: 670 sheet: -2.03 (0.24), residues: 391 loop : -2.53 (0.19), residues: 944 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 1.945 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 176 average time/residue: 0.2936 time to fit residues: 77.5569 Evaluate side-chains 131 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.757 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1338 time to fit residues: 2.5861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 181 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN E 184 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5641 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 15821 Z= 0.282 Angle : 0.691 11.212 21458 Z= 0.361 Chirality : 0.046 0.215 2451 Planarity : 0.005 0.050 2716 Dihedral : 6.328 102.631 2188 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -2.65 (0.18), residues: 2005 helix: -0.86 (0.19), residues: 672 sheet: -1.95 (0.24), residues: 392 loop : -2.32 (0.19), residues: 941 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.740 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 150 average time/residue: 0.2662 time to fit residues: 63.0055 Evaluate side-chains 121 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1398 time to fit residues: 2.7380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 132 optimal weight: 40.0000 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5684 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 15821 Z= 0.329 Angle : 0.736 11.240 21458 Z= 0.382 Chirality : 0.047 0.259 2451 Planarity : 0.005 0.081 2716 Dihedral : 6.507 100.797 2188 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -2.69 (0.17), residues: 2005 helix: -0.98 (0.18), residues: 662 sheet: -1.93 (0.24), residues: 399 loop : -2.27 (0.19), residues: 944 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.765 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 151 average time/residue: 0.2736 time to fit residues: 64.1267 Evaluate side-chains 112 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.864 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1537 time to fit residues: 2.8373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 0.9980 chunk 173 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 15821 Z= 0.218 Angle : 0.661 11.150 21458 Z= 0.342 Chirality : 0.045 0.198 2451 Planarity : 0.005 0.065 2716 Dihedral : 6.113 102.393 2188 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -2.38 (0.18), residues: 2005 helix: -0.64 (0.19), residues: 677 sheet: -1.87 (0.25), residues: 406 loop : -2.10 (0.20), residues: 922 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2810 time to fit residues: 70.1226 Evaluate side-chains 127 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 0.1980 chunk 140 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 162 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 191 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 393 ASN A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5509 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15821 Z= 0.192 Angle : 0.627 11.045 21458 Z= 0.324 Chirality : 0.043 0.190 2451 Planarity : 0.004 0.047 2716 Dihedral : 5.846 102.527 2188 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -2.08 (0.18), residues: 2005 helix: -0.37 (0.19), residues: 676 sheet: -1.72 (0.25), residues: 396 loop : -1.95 (0.20), residues: 933 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 1.669 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 165 average time/residue: 0.2724 time to fit residues: 69.6890 Evaluate side-chains 130 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 30.0000 chunk 57 optimal weight: 0.0030 chunk 37 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5593 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 15821 Z= 0.262 Angle : 0.688 11.561 21458 Z= 0.356 Chirality : 0.046 0.252 2451 Planarity : 0.005 0.066 2716 Dihedral : 6.100 101.938 2188 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -2.19 (0.18), residues: 2005 helix: -0.57 (0.19), residues: 666 sheet: -1.71 (0.25), residues: 404 loop : -1.93 (0.20), residues: 935 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 1.763 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2649 time to fit residues: 64.3763 Evaluate side-chains 120 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 161 optimal weight: 30.0000 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 189 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 423 GLN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5465 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 15821 Z= 0.177 Angle : 0.619 10.781 21458 Z= 0.318 Chirality : 0.043 0.225 2451 Planarity : 0.004 0.045 2716 Dihedral : 5.671 103.205 2188 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -1.89 (0.18), residues: 2005 helix: -0.17 (0.19), residues: 672 sheet: -1.63 (0.25), residues: 405 loop : -1.84 (0.20), residues: 928 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 1.800 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 167 average time/residue: 0.2783 time to fit residues: 74.4167 Evaluate side-chains 124 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.731 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1602 time to fit residues: 3.6486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 131 optimal weight: 0.0770 chunk 198 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 overall best weight: 2.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 423 GLN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5546 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 15821 Z= 0.239 Angle : 0.666 12.847 21458 Z= 0.342 Chirality : 0.044 0.232 2451 Planarity : 0.005 0.063 2716 Dihedral : 5.796 102.521 2188 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -1.99 (0.18), residues: 2005 helix: -0.41 (0.19), residues: 671 sheet: -1.56 (0.25), residues: 403 loop : -1.84 (0.20), residues: 931 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 1.846 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.2921 time to fit residues: 71.8077 Evaluate side-chains 121 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.864 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1837 time to fit residues: 2.6547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 158 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 138 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 423 GLN ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 ASN ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.171963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.144432 restraints weight = 59826.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.146433 restraints weight = 84296.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.147717 restraints weight = 54154.485| |-----------------------------------------------------------------------------| r_work (final): 0.4438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4438 r_free = 0.4438 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4437 r_free = 0.4437 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.4437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 15821 Z= 0.163 Angle : 0.612 10.517 21458 Z= 0.312 Chirality : 0.043 0.244 2451 Planarity : 0.004 0.045 2716 Dihedral : 5.530 103.462 2188 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.45 % 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: -1.65 (0.18), residues: 2005 helix: 0.01 (0.20), residues: 655 sheet: -1.46 (0.25), residues: 403 loop : -1.68 (0.20), residues: 947 =============================================================================== Job complete usr+sys time: 2897.58 seconds wall clock time: 54 minutes 39.20 seconds (3279.20 seconds total)