Starting phenix.real_space_refine on Sat Mar 16 19:37:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/03_2024/7niu_12365_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/03_2024/7niu_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_12365/03_2024/7niu_12365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/03_2024/7niu_12365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/03_2024/7niu_12365_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7niu_12365/03_2024/7niu_12365_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.76, per 1000 atoms: 0.63 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: 6.12 Conformation dependent library (CDL) restraints added in 3.4 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: 3.70 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: 5.67 Time building geometry restraints manager: 6.65 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: 8302 17.87 - 35.74: 973 35.74 - 53.62: 198 53.62 - 71.49: 41 71.49 - 89.36: 17 Dihedral angle restraints: 9531 sinusoidal: 3713 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 9528 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: 7.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 19.740 Check model and map are aligned: 0.290 Set scattering table: 0.130 Process input model: 45.180 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.650 ------------------------------------------------------------------------------- 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 : 16.083 89.361 5783 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 % Allowed : 12.57 % Favored : 85.77 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 164 HIS 0.006 0.002 HIS A 67 PHE 0.052 0.003 PHE A 305 TYR 0.030 0.003 TYR A 919 ARG 0.008 0.001 ARG A1191 *********************** 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 : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 ARG cc_start: 0.6126 (mtm180) cc_final: 0.5842 (mtp180) REVERT: A 469 ARG cc_start: 0.6506 (mtt90) cc_final: 0.3949 (ptp-110) REVERT: A 577 LYS cc_start: 0.6404 (OUTLIER) cc_final: 0.5774 (pttt) REVERT: A 618 MET cc_start: 0.2221 (ttt) cc_final: 0.1458 (mtp) REVERT: A 704 ASN cc_start: 0.6940 (p0) cc_final: 0.6606 (p0) REVERT: A 975 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6112 (tp) REVERT: E 97 TYR cc_start: 0.4188 (m-10) cc_final: 0.3515 (m-10) REVERT: E 108 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.5830 (tp40) REVERT: B 5 MET cc_start: 0.3819 (tpp) cc_final: 0.2865 (pmm) outliers start: 27 outliers final: 13 residues processed: 211 average time/residue: 0.3302 time to fit residues: 99.0254 Evaluate side-chains 136 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.628 ------------------------------------------------------------------------------- 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: 7.9990 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 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 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 A 965 ASN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN A1231 HIS D 7 GLN D 91 GLN E 108 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5613 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15821 Z= 0.249 Angle : 0.703 13.567 21458 Z= 0.368 Chirality : 0.046 0.233 2451 Planarity : 0.005 0.051 2716 Dihedral : 6.935 55.112 2300 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.48 % Allowed : 6.37 % Favored : 93.15 % 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: -3.72 (0.16), residues: 2005 helix: -1.86 (0.17), residues: 682 sheet: -2.48 (0.23), residues: 413 loop : -2.89 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 164 HIS 0.009 0.001 HIS A 385 PHE 0.022 0.002 PHE A 697 TYR 0.028 0.002 TYR A 937 ARG 0.005 0.001 ARG A1109 *********************** 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 190 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7006 (mmm) cc_final: 0.6185 (mmm) REVERT: A 116 TYR cc_start: 0.5392 (m-80) cc_final: 0.5019 (m-80) REVERT: A 406 ARG cc_start: 0.6117 (mtm180) cc_final: 0.5695 (mtp180) REVERT: A 618 MET cc_start: 0.2884 (ttt) cc_final: 0.2274 (mtp) REVERT: A 704 ASN cc_start: 0.6820 (p0) cc_final: 0.6436 (p0) REVERT: A 975 LEU cc_start: 0.5863 (tp) cc_final: 0.5591 (tp) REVERT: E 73 ILE cc_start: 0.4940 (tp) cc_final: 0.4558 (tt) REVERT: B 5 MET cc_start: 0.3547 (tpp) cc_final: 0.2659 (pmm) outliers start: 7 outliers final: 0 residues processed: 187 average time/residue: 0.3130 time to fit residues: 87.2076 Evaluate side-chains 137 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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: 7.9990 chunk 150 optimal weight: 40.0000 chunk 123 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 806 HIS ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 GLN ** A1152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15821 Z= 0.375 Angle : 0.793 11.305 21458 Z= 0.413 Chirality : 0.049 0.252 2451 Planarity : 0.005 0.050 2716 Dihedral : 7.032 54.361 2300 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 0.42 % Allowed : 6.67 % Favored : 92.91 % 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: -3.39 (0.17), residues: 2005 helix: -1.63 (0.18), residues: 665 sheet: -2.24 (0.24), residues: 400 loop : -2.67 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 112 HIS 0.006 0.001 HIS E 38 PHE 0.026 0.003 PHE A 956 TYR 0.034 0.003 TYR A 949 ARG 0.006 0.001 ARG A 788 *********************** 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 158 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 1.863 Fit side-chains REVERT: A 54 LYS cc_start: 0.7566 (mttt) cc_final: 0.6815 (mmtt) REVERT: A 113 MET cc_start: 0.6968 (mmm) cc_final: 0.5979 (mmm) REVERT: A 406 ARG cc_start: 0.6104 (mtm180) cc_final: 0.5771 (mtp180) REVERT: A 446 TYR cc_start: 0.7098 (m-80) cc_final: 0.6793 (m-80) REVERT: A 469 ARG cc_start: 0.6691 (mtt90) cc_final: 0.6161 (mtt180) REVERT: A 499 MET cc_start: 0.6251 (mmm) cc_final: 0.5950 (mmt) REVERT: A 618 MET cc_start: 0.2791 (ttt) cc_final: 0.1994 (mtp) REVERT: A 704 ASN cc_start: 0.6963 (p0) cc_final: 0.6623 (p0) REVERT: A 975 LEU cc_start: 0.6367 (tp) cc_final: 0.6159 (tp) REVERT: B 5 MET cc_start: 0.3636 (tpp) cc_final: 0.2756 (pmm) outliers start: 6 outliers final: 2 residues processed: 157 average time/residue: 0.3015 time to fit residues: 69.7200 Evaluate side-chains 117 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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: 5.9990 chunk 136 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 181 optimal weight: 0.5980 chunk 192 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 ASN ** A1194 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5649 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15821 Z= 0.267 Angle : 0.701 11.069 21458 Z= 0.365 Chirality : 0.046 0.234 2451 Planarity : 0.005 0.050 2716 Dihedral : 6.546 57.545 2300 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.24 % Allowed : 5.00 % Favored : 94.76 % 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: -2.87 (0.18), residues: 2005 helix: -1.14 (0.19), residues: 673 sheet: -2.02 (0.25), residues: 397 loop : -2.38 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 164 HIS 0.006 0.001 HIS E 38 PHE 0.028 0.002 PHE A 305 TYR 0.025 0.002 TYR A 927 ARG 0.008 0.001 ARG A 444 *********************** 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 164 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 ARG cc_start: 0.6007 (mtm180) cc_final: 0.5667 (mtp180) REVERT: A 499 MET cc_start: 0.6191 (mmm) cc_final: 0.5913 (mmt) REVERT: A 618 MET cc_start: 0.2330 (ttt) cc_final: 0.1553 (mtp) REVERT: A 975 LEU cc_start: 0.6173 (tp) cc_final: 0.5774 (tp) REVERT: E 73 ILE cc_start: 0.5003 (tp) cc_final: 0.4455 (tt) REVERT: B 5 MET cc_start: 0.3509 (tpp) cc_final: 0.2623 (pmm) outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 0.2666 time to fit residues: 65.5365 Evaluate side-chains 122 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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: 20.0000 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 172 optimal weight: 40.0000 chunk 48 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 385 HIS ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 539 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 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 ASN ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 15821 Z= 0.385 Angle : 0.803 11.477 21458 Z= 0.417 Chirality : 0.050 0.283 2451 Planarity : 0.006 0.090 2716 Dihedral : 6.954 55.492 2300 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.24 % Allowed : 5.66 % Favored : 94.10 % 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: -3.01 (0.17), residues: 2005 helix: -1.45 (0.18), residues: 673 sheet: -1.97 (0.25), residues: 390 loop : -2.36 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 112 HIS 0.007 0.001 HIS E 38 PHE 0.042 0.003 PHE A 305 TYR 0.023 0.003 TYR A 132 ARG 0.008 0.001 ARG A 444 *********************** 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 150 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7594 (mttt) cc_final: 0.6808 (mmtt) REVERT: A 113 MET cc_start: 0.6855 (mmm) cc_final: 0.6193 (mmm) REVERT: A 147 ARG cc_start: 0.7266 (ppt170) cc_final: 0.6741 (ttt180) REVERT: A 334 MET cc_start: 0.7108 (mmm) cc_final: 0.6908 (mmm) REVERT: A 406 ARG cc_start: 0.5954 (mtm180) cc_final: 0.5666 (mtp180) REVERT: A 469 ARG cc_start: 0.6630 (mtt90) cc_final: 0.6181 (mtt180) REVERT: A 499 MET cc_start: 0.6265 (mmm) cc_final: 0.5985 (mmt) REVERT: A 618 MET cc_start: 0.2375 (ttt) cc_final: 0.1388 (mtp) REVERT: A 704 ASN cc_start: 0.7046 (p0) cc_final: 0.6743 (p0) REVERT: A 887 LYS cc_start: 0.7582 (tmmt) cc_final: 0.6393 (mttt) REVERT: E 73 ILE cc_start: 0.5076 (tp) cc_final: 0.4762 (tt) outliers start: 2 outliers final: 1 residues processed: 149 average time/residue: 0.2994 time to fit residues: 68.0000 Evaluate side-chains 121 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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: 0.9990 chunk 173 optimal weight: 40.0000 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 159 optimal weight: 30.0000 chunk 89 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 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 929 ASN ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 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: 0.5474 moved from start: 0.3505 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= 0.175 Angle : 0.628 10.764 21458 Z= 0.326 Chirality : 0.043 0.190 2451 Planarity : 0.004 0.051 2716 Dihedral : 5.819 56.122 2300 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.18 % Allowed : 2.92 % Favored : 96.90 % 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: -2.31 (0.18), residues: 2005 helix: -0.61 (0.19), residues: 677 sheet: -1.89 (0.25), residues: 405 loop : -2.02 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 164 HIS 0.004 0.001 HIS E 38 PHE 0.022 0.002 PHE B 72 TYR 0.025 0.002 TYR D 141 ARG 0.007 0.001 ARG E 110 *********************** 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 180 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6514 (mmm) cc_final: 0.6193 (tmm) REVERT: A 194 MET cc_start: 0.7648 (tpp) cc_final: 0.7175 (tpt) REVERT: A 406 ARG cc_start: 0.5793 (mtm180) cc_final: 0.5478 (mtp180) REVERT: A 469 ARG cc_start: 0.6479 (mtt90) cc_final: 0.3420 (ptp-110) REVERT: A 499 MET cc_start: 0.6079 (mmm) cc_final: 0.5797 (mmt) REVERT: A 618 MET cc_start: 0.2303 (ttt) cc_final: 0.1528 (mtp) REVERT: E 73 ILE cc_start: 0.4875 (tp) cc_final: 0.4551 (tt) REVERT: C 174 TRP cc_start: 0.3062 (m100) cc_final: 0.2744 (m-90) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2670 time to fit residues: 72.3248 Evaluate side-chains 134 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.796 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 0.0470 chunk 140 optimal weight: 0.3980 chunk 108 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 overall best weight: 2.0682 ------------------------------------------------------------------------------- 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 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 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15821 Z= 0.222 Angle : 0.651 11.228 21458 Z= 0.337 Chirality : 0.044 0.200 2451 Planarity : 0.005 0.054 2716 Dihedral : 5.770 58.434 2300 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.12 % Allowed : 2.44 % Favored : 97.44 % 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: -2.24 (0.18), residues: 2005 helix: -0.56 (0.19), residues: 677 sheet: -1.81 (0.25), residues: 405 loop : -1.97 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 164 HIS 0.006 0.001 HIS E 38 PHE 0.034 0.002 PHE A 305 TYR 0.034 0.002 TYR C 58 ARG 0.004 0.000 ARG A 788 *********************** 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 171 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6825 (mmm) cc_final: 0.6208 (mmm) REVERT: A 116 TYR cc_start: 0.5395 (m-80) cc_final: 0.5078 (m-80) REVERT: A 406 ARG cc_start: 0.5875 (mtm180) cc_final: 0.5500 (mtp180) REVERT: A 499 MET cc_start: 0.6128 (mmm) cc_final: 0.5825 (mmt) REVERT: A 618 MET cc_start: 0.2413 (ttt) cc_final: 0.1500 (mtp) REVERT: E 73 ILE cc_start: 0.4915 (tp) cc_final: 0.4600 (tt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2617 time to fit residues: 67.8512 Evaluate side-chains 128 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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: 20.0000 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 40.0000 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 130 optimal weight: 50.0000 chunk 94 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15821 Z= 0.207 Angle : 0.636 11.148 21458 Z= 0.330 Chirality : 0.044 0.251 2451 Planarity : 0.004 0.047 2716 Dihedral : 5.555 55.568 2300 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.12 % Allowed : 1.67 % Favored : 98.21 % 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: -2.09 (0.18), residues: 2005 helix: -0.45 (0.19), residues: 669 sheet: -1.70 (0.25), residues: 405 loop : -1.88 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 112 HIS 0.005 0.001 HIS E 38 PHE 0.018 0.002 PHE A 970 TYR 0.029 0.002 TYR C 58 ARG 0.004 0.000 ARG A 788 *********************** 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 171 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7066 (mmm) cc_final: 0.6564 (mmm) REVERT: A 116 TYR cc_start: 0.5382 (m-80) cc_final: 0.5134 (m-80) REVERT: A 221 MET cc_start: 0.5314 (tmm) cc_final: 0.4682 (tmm) REVERT: A 406 ARG cc_start: 0.5923 (mtm180) cc_final: 0.5467 (mtp180) REVERT: A 499 MET cc_start: 0.6111 (mmm) cc_final: 0.5830 (mmt) REVERT: A 618 MET cc_start: 0.2437 (ttt) cc_final: 0.1542 (mtp) REVERT: E 73 ILE cc_start: 0.4915 (tp) cc_final: 0.4587 (tt) REVERT: C 174 TRP cc_start: 0.2922 (m100) cc_final: 0.2575 (m100) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2766 time to fit residues: 73.7154 Evaluate side-chains 124 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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: 8.9990 chunk 167 optimal weight: 30.0000 chunk 178 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 140 optimal weight: 0.4980 chunk 54 optimal weight: 0.4980 chunk 161 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 189 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 280 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 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** ** A1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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: 0.5553 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15821 Z= 0.232 Angle : 0.658 11.607 21458 Z= 0.339 Chirality : 0.044 0.237 2451 Planarity : 0.004 0.055 2716 Dihedral : 5.569 55.722 2300 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.24 % Allowed : 1.19 % Favored : 98.57 % 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: -2.03 (0.18), residues: 2005 helix: -0.44 (0.19), residues: 666 sheet: -1.66 (0.25), residues: 401 loop : -1.81 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 112 HIS 0.006 0.001 HIS E 38 PHE 0.036 0.002 PHE A 305 TYR 0.023 0.002 TYR A 132 ARG 0.004 0.000 ARG A 278 *********************** 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 164 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7038 (mmm) cc_final: 0.5950 (mmm) REVERT: A 116 TYR cc_start: 0.5447 (m-80) cc_final: 0.5108 (m-80) REVERT: A 406 ARG cc_start: 0.5839 (mtm180) cc_final: 0.5477 (mtp180) REVERT: A 499 MET cc_start: 0.6122 (mmm) cc_final: 0.5790 (mmt) REVERT: A 618 MET cc_start: 0.2650 (ttt) cc_final: 0.1562 (mtp) REVERT: A 800 MET cc_start: 0.8075 (tpt) cc_final: 0.7720 (tpt) REVERT: A 887 LYS cc_start: 0.7386 (tmmt) cc_final: 0.6183 (mttt) REVERT: E 73 ILE cc_start: 0.4964 (tp) cc_final: 0.4610 (tt) REVERT: E 110 ARG cc_start: 0.7097 (ttm110) cc_final: 0.6800 (ttm110) outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.2609 time to fit residues: 65.6671 Evaluate side-chains 121 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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: 5.9990 chunk 89 optimal weight: 0.0060 chunk 131 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 125 optimal weight: 30.0000 chunk 168 optimal weight: 30.0000 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 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 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** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5563 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15821 Z= 0.243 Angle : 0.672 13.789 21458 Z= 0.345 Chirality : 0.045 0.228 2451 Planarity : 0.004 0.052 2716 Dihedral : 5.639 55.128 2300 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.18 % Allowed : 0.54 % Favored : 99.29 % 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: -2.10 (0.18), residues: 2005 helix: -0.62 (0.19), residues: 679 sheet: -1.60 (0.25), residues: 399 loop : -1.81 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 39 HIS 0.005 0.001 HIS E 38 PHE 0.031 0.002 PHE A 316 TYR 0.022 0.002 TYR A 132 ARG 0.004 0.000 ARG A 788 ********************** 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 155 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7409 (mttt) cc_final: 0.6607 (mmtt) REVERT: A 113 MET cc_start: 0.6901 (mmm) cc_final: 0.6109 (mmm) REVERT: A 116 TYR cc_start: 0.5508 (m-80) cc_final: 0.5090 (m-80) REVERT: A 301 MET cc_start: 0.7161 (tpt) cc_final: 0.6591 (tpt) REVERT: A 406 ARG cc_start: 0.5917 (mtm180) cc_final: 0.5514 (mtp180) REVERT: A 499 MET cc_start: 0.6138 (mmm) cc_final: 0.5805 (mmt) REVERT: A 618 MET cc_start: 0.2554 (ttt) cc_final: 0.1519 (mtp) REVERT: A 800 MET cc_start: 0.8092 (tpt) cc_final: 0.7717 (tpt) REVERT: A 820 ASP cc_start: 0.6694 (m-30) cc_final: 0.6454 (m-30) REVERT: A 887 LYS cc_start: 0.7360 (tmmt) cc_final: 0.6132 (mttt) REVERT: E 73 ILE cc_start: 0.4967 (tp) cc_final: 0.4621 (tt) REVERT: E 110 ARG cc_start: 0.7125 (ttm110) cc_final: 0.6858 (ttm110) REVERT: C 174 TRP cc_start: 0.3071 (m100) cc_final: 0.2767 (m100) outliers start: 1 outliers final: 1 residues processed: 155 average time/residue: 0.2718 time to fit residues: 64.5822 Evaluate side-chains 120 residues out of total 1671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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: 5.9990 chunk 145 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 138 optimal weight: 30.0000 chunk 9 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 HIS ** B 91 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.172530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.147593 restraints weight = 60006.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.150085 restraints weight = 96595.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.150625 restraints weight = 59449.904| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4460 r_free = 0.4460 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4459 r_free = 0.4459 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5602 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15821 Z= 0.165 Angle : 0.612 10.690 21458 Z= 0.314 Chirality : 0.042 0.271 2451 Planarity : 0.004 0.046 2716 Dihedral : 5.239 50.613 2300 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.12 % Allowed : 0.60 % Favored : 99.29 % 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: -1.75 (0.19), residues: 2005 helix: -0.17 (0.20), residues: 670 sheet: -1.52 (0.25), residues: 401 loop : -1.68 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 39 HIS 0.005 0.001 HIS E 38 PHE 0.034 0.002 PHE A 85 TYR 0.019 0.001 TYR A 852 ARG 0.004 0.000 ARG A 971 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3017.83 seconds wall clock time: 56 minutes 21.09 seconds (3381.09 seconds total)