Starting phenix.real_space_refine on Thu Feb 15 07:08:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roj_4974/02_2024/6roj_4974_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roj_4974/02_2024/6roj_4974.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roj_4974/02_2024/6roj_4974_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roj_4974/02_2024/6roj_4974_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roj_4974/02_2024/6roj_4974_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roj_4974/02_2024/6roj_4974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roj_4974/02_2024/6roj_4974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roj_4974/02_2024/6roj_4974_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6roj_4974/02_2024/6roj_4974_updated.pdb" } resolution = 2.9 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= 0.002 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: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 47 5.16 5 Be 1 3.05 5 C 7407 2.51 5 N 1842 2.21 5 O 2162 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 189": "OD1" <-> "OD2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ASP 584": "OD1" <-> "OD2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A ASP 625": "OD1" <-> "OD2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A ARG 866": "NH1" <-> "NH2" Residue "A ASP 868": "OD1" <-> "OD2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ASP 984": "OD1" <-> "OD2" Residue "A TYR 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 262": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11465 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8508 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2761 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 21, 'TRANS': 318} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 68 Unusual residues: {' MG': 1, '2Y5': 1} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Time building chain proxies: 6.56, per 1000 atoms: 0.57 Number of scatterers: 11465 At special positions: 0 Unit cell: (80.775, 105.546, 173.397, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 47 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 2162 8.00 N 1842 7.00 C 7407 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.04 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 Links applied BETA1-3 " BMA B 3 " - " BMA B 4 " " BMA E 3 " - " BMA E 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG D 1 " - " ASN C 216 " " NAG E 1 " - " ASN C 199 " Time building additional restraints: 4.46 Conformation dependent library (CDL) restraints added in 2.1 seconds 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2658 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 12 sheets defined 38.3% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 213 through 221 removed outlier: 4.063A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 251 through 280 removed outlier: 3.573A pdb=" N SER A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.520A pdb=" N ASN A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 505 removed outlier: 4.348A pdb=" N LEU A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASN A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.693A pdb=" N MET A 524 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 619 through 632 removed outlier: 3.654A pdb=" N ILE A 623 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR A 628 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 630 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 632 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.635A pdb=" N LEU A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.898A pdb=" N LEU A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG A 730 " --> pdb=" O VAL A 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 724 through 730' Processing helix chain 'A' and resid 739 through 750 removed outlier: 3.575A pdb=" N ARG A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 781 removed outlier: 3.524A pdb=" N GLU A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 817 through 826 Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.521A pdb=" N SER A 848 " --> pdb=" O ASN A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 881 removed outlier: 3.603A pdb=" N GLU A 870 " --> pdb=" O ARG A 866 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 881 " --> pdb=" O ILE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 911 through 918 Processing helix chain 'A' and resid 933 through 944 removed outlier: 4.006A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 944 " --> pdb=" O MET A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 963 removed outlier: 4.039A pdb=" N VAL A 959 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER A 960 " --> pdb=" O ASN A 957 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET A 961 " --> pdb=" O ASP A 958 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 981 No H-bonds generated for 'chain 'A' and resid 978 through 981' Processing helix chain 'A' and resid 990 through 998 removed outlier: 3.545A pdb=" N LYS A 994 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 995 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 996 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 997 " --> pdb=" O LYS A 994 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 998 " --> pdb=" O LYS A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1023 removed outlier: 3.968A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1056 through 1064 Processing helix chain 'A' and resid 1070 through 1075 removed outlier: 3.576A pdb=" N GLU A1074 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A1075 " --> pdb=" O ARG A1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1070 through 1075' Processing helix chain 'A' and resid 1077 through 1085 removed outlier: 3.573A pdb=" N LEU A1082 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A1083 " --> pdb=" O TYR A1080 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A1084 " --> pdb=" O LYS A1081 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A1085 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1115 removed outlier: 3.841A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A1097 " --> pdb=" O ILE A1093 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1114 " --> pdb=" O ILE A1110 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A1115 " --> pdb=" O GLY A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1153 removed outlier: 4.237A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A1150 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A1152 " --> pdb=" O GLY A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1182 removed outlier: 3.520A pdb=" N ILE A1174 " --> pdb=" O LEU A1170 " (cutoff:3.500A) Proline residue: A1177 - end of helix removed outlier: 4.068A pdb=" N SER A1181 " --> pdb=" O PRO A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1186 No H-bonds generated for 'chain 'A' and resid 1184 through 1186' Processing helix chain 'A' and resid 1195 through 1199 Processing helix chain 'A' and resid 1205 through 1216 removed outlier: 4.187A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) Proline residue: A1213 - end of helix Processing helix chain 'A' and resid 1218 through 1230 removed outlier: 3.611A pdb=" N ARG A1228 " --> pdb=" O LYS A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1244 removed outlier: 3.843A pdb=" N ILE A1238 " --> pdb=" O THR A1234 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 68 removed outlier: 3.645A pdb=" N LEU C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Proline residue: C 47 - end of helix Proline residue: C 58 - end of helix removed outlier: 3.530A pdb=" N SER C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 83 No H-bonds generated for 'chain 'C' and resid 80 through 83' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.626A pdb=" N LEU C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 331 through 356 removed outlier: 3.770A pdb=" N LEU C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= B, first strand: chain 'A' and resid 283 through 288 removed outlier: 3.756A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 307 through 310 removed outlier: 3.714A pdb=" N VAL A 310 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.755A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 385 through 387 Processing sheet with id= F, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.521A pdb=" N TYR A 556 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE A 952 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A 558 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS A 830 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N SER A 559 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP A 832 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 924 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 923 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN A 857 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL A 896 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU A 859 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 637 through 639 Processing sheet with id= H, first strand: chain 'A' and resid 667 through 669 Processing sheet with id= I, first strand: chain 'A' and resid 570 through 577 removed outlier: 6.661A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 706 " --> pdb=" O CYS A 696 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 694 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.408A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 113 through 115 Processing sheet with id= L, first strand: chain 'C' and resid 207 through 209 removed outlier: 4.436A pdb=" N LYS C 297 " --> pdb=" O ILE C 209 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 978 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: 3.67 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1846 1.31 - 1.43: 3185 1.43 - 1.56: 6610 1.56 - 1.69: 8 1.69 - 1.81: 75 Bond restraints: 11724 Sorted by residual: bond pdb=" OD1 BFD A 560 " pdb="BE BFD A 560 " ideal model delta sigma weight residual 1.737 1.530 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.516 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.511 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C1 BMA B 4 " pdb=" C2 BMA B 4 " ideal model delta sigma weight residual 1.519 1.572 -0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C GLU A 327 " pdb=" N PRO A 328 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.20e-02 6.94e+03 4.85e+00 ... (remaining 11719 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.91: 217 105.91 - 113.13: 6413 113.13 - 120.35: 4690 120.35 - 127.56: 4461 127.56 - 134.78: 115 Bond angle restraints: 15896 Sorted by residual: angle pdb=" C21 2Y5 A1502 " pdb=" C22 2Y5 A1502 " pdb=" C23 2Y5 A1502 " ideal model delta sigma weight residual 85.82 121.61 -35.79 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C18 2Y5 A1502 " pdb=" C19 2Y5 A1502 " pdb=" C20 2Y5 A1502 " ideal model delta sigma weight residual 152.65 121.98 30.67 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C15 2Y5 A1502 " pdb=" C16 2Y5 A1502 " pdb=" C17 2Y5 A1502 " ideal model delta sigma weight residual 152.62 122.40 30.22 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C24 2Y5 A1502 " pdb=" C25 2Y5 A1502 " pdb=" C26 2Y5 A1502 " ideal model delta sigma weight residual 152.70 122.52 30.18 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C VAL A 929 " pdb=" N SER A 930 " pdb=" CA SER A 930 " ideal model delta sigma weight residual 120.86 128.04 -7.18 1.60e+00 3.91e-01 2.01e+01 ... (remaining 15891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 6926 35.28 - 70.56: 142 70.56 - 105.84: 39 105.84 - 141.12: 6 141.12 - 176.40: 2 Dihedral angle restraints: 7115 sinusoidal: 2994 harmonic: 4121 Sorted by residual: dihedral pdb=" CB CYS C 176 " pdb=" SG CYS C 176 " pdb=" SG CYS C 190 " pdb=" CB CYS C 190 " ideal model delta sinusoidal sigma weight residual 93.00 154.31 -61.31 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CA TYR C 236 " pdb=" C TYR C 236 " pdb=" N ASN C 237 " pdb=" CA ASN C 237 " ideal model delta harmonic sigma weight residual 180.00 153.02 26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta harmonic sigma weight residual 180.00 -153.08 -26.92 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 7112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1585 0.078 - 0.157: 221 0.157 - 0.235: 18 0.235 - 0.313: 4 0.313 - 0.392: 1 Chirality restraints: 1829 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.74e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN C 288 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1826 not shown) Planarity restraints: 1981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 111 " 0.032 2.00e-02 2.50e+03 2.79e-02 1.94e+01 pdb=" CG TRP C 111 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP C 111 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP C 111 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 111 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 111 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 111 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1057 " 0.052 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A1058 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A1058 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1058 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 673 " -0.047 5.00e-02 4.00e+02 6.99e-02 7.83e+00 pdb=" N PRO A 674 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 674 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 674 " -0.039 5.00e-02 4.00e+02 ... (remaining 1978 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 13 2.34 - 2.98: 5392 2.98 - 3.62: 16223 3.62 - 4.26: 27249 4.26 - 4.90: 44850 Nonbonded interactions: 93727 Sorted by model distance: nonbonded pdb=" F2 BFD A 560 " pdb="MG MG A1501 " model vdw 1.705 2.120 nonbonded pdb="MG MG A1501 " pdb=" O HOH A1602 " model vdw 1.884 2.170 nonbonded pdb="MG MG A1501 " pdb=" O HOH A1601 " model vdw 1.916 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1501 " model vdw 2.056 2.170 nonbonded pdb=" OD2 BFD A 560 " pdb="MG MG A1501 " model vdw 2.111 2.170 ... (remaining 93722 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' selection = chain 'E' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 3.980 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 32.860 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.006 0.207 11724 Z= 0.409 Angle : 1.071 35.793 15896 Z= 0.549 Chirality : 0.056 0.392 1829 Planarity : 0.007 0.077 1978 Dihedral : 17.311 176.397 4451 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.16 % Allowed : 5.87 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.17), residues: 1397 helix: -4.55 (0.08), residues: 596 sheet: -1.72 (0.32), residues: 212 loop : -2.15 (0.22), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP C 111 HIS 0.007 0.001 HIS A 634 PHE 0.029 0.002 PHE A 711 TYR 0.031 0.002 TYR C 236 ARG 0.009 0.001 ARG A1219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.7693 (tpt) cc_final: 0.7315 (tmt) REVERT: A 726 VAL cc_start: 0.8467 (p) cc_final: 0.8267 (p) REVERT: A 891 ASN cc_start: 0.8313 (m110) cc_final: 0.7629 (t0) REVERT: A 1241 MET cc_start: 0.8562 (mtt) cc_final: 0.8352 (mtt) outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 1.3878 time to fit residues: 162.4651 Evaluate side-chains 66 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 399 GLN A 649 GLN A 675 ASN A 891 ASN A1187 ASN C 30 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11724 Z= 0.186 Angle : 0.624 11.910 15896 Z= 0.315 Chirality : 0.044 0.254 1829 Planarity : 0.005 0.050 1978 Dihedral : 14.400 170.077 1759 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.29 % Allowed : 10.45 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.19), residues: 1397 helix: -2.88 (0.15), residues: 596 sheet: -1.40 (0.33), residues: 216 loop : -1.67 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 111 HIS 0.003 0.001 HIS A 634 PHE 0.015 0.001 PHE A1094 TYR 0.019 0.001 TYR C 236 ARG 0.004 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 675 ASN cc_start: 0.7938 (m110) cc_final: 0.7257 (p0) outliers start: 16 outliers final: 5 residues processed: 82 average time/residue: 1.1666 time to fit residues: 105.5808 Evaluate side-chains 66 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN A 399 GLN A1084 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11724 Z= 0.235 Angle : 0.601 12.800 15896 Z= 0.298 Chirality : 0.043 0.170 1829 Planarity : 0.004 0.043 1978 Dihedral : 11.560 154.261 1759 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.93 % Allowed : 12.86 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.21), residues: 1397 helix: -1.81 (0.19), residues: 609 sheet: -1.06 (0.34), residues: 210 loop : -1.31 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 111 HIS 0.004 0.001 HIS A1198 PHE 0.016 0.001 PHE A1205 TYR 0.020 0.001 TYR A 738 ARG 0.003 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 570 MET cc_start: 0.8018 (mtp) cc_final: 0.7731 (mtp) REVERT: A 675 ASN cc_start: 0.7908 (m110) cc_final: 0.7269 (p0) REVERT: A 804 ILE cc_start: 0.9167 (mt) cc_final: 0.8853 (mp) outliers start: 24 outliers final: 13 residues processed: 84 average time/residue: 1.1851 time to fit residues: 109.5657 Evaluate side-chains 78 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 1024 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.0020 chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.9350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN A1084 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11724 Z= 0.199 Angle : 0.554 12.639 15896 Z= 0.277 Chirality : 0.042 0.166 1829 Planarity : 0.004 0.042 1978 Dihedral : 10.343 148.962 1759 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.77 % Allowed : 14.87 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.22), residues: 1397 helix: -1.24 (0.20), residues: 599 sheet: -0.86 (0.35), residues: 208 loop : -1.08 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 111 HIS 0.004 0.001 HIS A 634 PHE 0.015 0.001 PHE A1205 TYR 0.018 0.001 TYR C 236 ARG 0.005 0.000 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 804 ILE cc_start: 0.9161 (mt) cc_final: 0.8852 (mp) REVERT: A 974 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6489 (ppp) REVERT: C 303 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7409 (mp0) outliers start: 22 outliers final: 13 residues processed: 81 average time/residue: 1.1926 time to fit residues: 106.7120 Evaluate side-chains 76 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 34 optimal weight: 0.0040 chunk 45 optimal weight: 0.9980 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 649 GLN A1084 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11724 Z= 0.289 Angle : 0.578 12.717 15896 Z= 0.292 Chirality : 0.044 0.160 1829 Planarity : 0.004 0.042 1978 Dihedral : 9.753 145.632 1759 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.33 % Allowed : 14.79 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.22), residues: 1397 helix: -0.99 (0.21), residues: 595 sheet: -0.81 (0.35), residues: 211 loop : -1.00 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 111 HIS 0.005 0.001 HIS A1198 PHE 0.017 0.001 PHE A1205 TYR 0.020 0.001 TYR C 236 ARG 0.003 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 65 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.8066 (mtp) cc_final: 0.7742 (mtp) REVERT: A 705 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6211 (tmt) REVERT: A 804 ILE cc_start: 0.9135 (mt) cc_final: 0.8796 (mp) REVERT: A 837 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7684 (m-30) REVERT: A 891 ASN cc_start: 0.8365 (m-40) cc_final: 0.7412 (t0) REVERT: A 974 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6653 (ppp) REVERT: C 303 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7441 (mp0) outliers start: 29 outliers final: 15 residues processed: 86 average time/residue: 1.0837 time to fit residues: 103.8399 Evaluate side-chains 80 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 649 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11724 Z= 0.179 Angle : 0.528 12.603 15896 Z= 0.267 Chirality : 0.042 0.162 1829 Planarity : 0.004 0.041 1978 Dihedral : 9.308 142.582 1759 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.17 % Allowed : 15.84 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), residues: 1397 helix: -0.75 (0.22), residues: 596 sheet: -0.64 (0.35), residues: 211 loop : -0.86 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.004 0.001 HIS A 634 PHE 0.013 0.001 PHE A1205 TYR 0.016 0.001 TYR C 236 ARG 0.003 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 460 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7997 (tp) REVERT: A 570 MET cc_start: 0.8005 (mtp) cc_final: 0.7676 (mtp) REVERT: A 705 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6227 (tmt) REVERT: A 804 ILE cc_start: 0.9114 (mt) cc_final: 0.8787 (mp) REVERT: A 891 ASN cc_start: 0.8343 (m-40) cc_final: 0.7357 (t0) REVERT: A 974 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6623 (ppp) outliers start: 27 outliers final: 15 residues processed: 88 average time/residue: 1.0826 time to fit residues: 106.2199 Evaluate side-chains 78 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11724 Z= 0.198 Angle : 0.539 12.633 15896 Z= 0.272 Chirality : 0.042 0.163 1829 Planarity : 0.004 0.041 1978 Dihedral : 9.211 142.286 1759 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.77 % Allowed : 16.56 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.23), residues: 1397 helix: -0.69 (0.22), residues: 602 sheet: -0.59 (0.35), residues: 211 loop : -0.83 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 111 HIS 0.003 0.001 HIS A 634 PHE 0.014 0.001 PHE A1205 TYR 0.017 0.001 TYR C 236 ARG 0.002 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 460 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8017 (tp) REVERT: A 570 MET cc_start: 0.8006 (mtp) cc_final: 0.7680 (mtp) REVERT: A 705 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6215 (tmt) REVERT: A 804 ILE cc_start: 0.9126 (mt) cc_final: 0.8814 (mp) REVERT: A 891 ASN cc_start: 0.8343 (m-40) cc_final: 0.7350 (t0) REVERT: A 974 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6678 (ppp) outliers start: 22 outliers final: 16 residues processed: 80 average time/residue: 1.0310 time to fit residues: 92.6429 Evaluate side-chains 78 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 59 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 0.0570 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11724 Z= 0.265 Angle : 0.560 12.651 15896 Z= 0.283 Chirality : 0.043 0.163 1829 Planarity : 0.004 0.042 1978 Dihedral : 9.207 141.513 1759 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.09 % Allowed : 16.40 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1397 helix: -0.73 (0.21), residues: 601 sheet: -0.61 (0.35), residues: 211 loop : -0.85 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 111 HIS 0.004 0.001 HIS A1198 PHE 0.016 0.001 PHE A1205 TYR 0.018 0.001 TYR C 236 ARG 0.002 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 62 time to evaluate : 1.460 Fit side-chains revert: symmetry clash REVERT: A 460 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8033 (tp) REVERT: A 570 MET cc_start: 0.7997 (mtp) cc_final: 0.7667 (mtp) REVERT: A 705 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6230 (tmt) REVERT: A 743 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7822 (mpt) REVERT: A 804 ILE cc_start: 0.9142 (mt) cc_final: 0.8828 (mp) REVERT: A 891 ASN cc_start: 0.8343 (m-40) cc_final: 0.7343 (t0) REVERT: A 974 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6709 (ppp) outliers start: 26 outliers final: 16 residues processed: 80 average time/residue: 1.0343 time to fit residues: 92.3860 Evaluate side-chains 79 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 5.9990 chunk 125 optimal weight: 0.0040 chunk 129 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11724 Z= 0.148 Angle : 0.515 12.594 15896 Z= 0.259 Chirality : 0.041 0.165 1829 Planarity : 0.003 0.041 1978 Dihedral : 8.858 141.728 1759 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.61 % Allowed : 17.12 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1397 helix: -0.53 (0.22), residues: 596 sheet: -0.54 (0.35), residues: 213 loop : -0.83 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1132 HIS 0.003 0.000 HIS A 634 PHE 0.012 0.001 PHE A1205 TYR 0.015 0.001 TYR C 236 ARG 0.003 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 570 MET cc_start: 0.7970 (mtp) cc_final: 0.7644 (mtp) REVERT: A 705 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6217 (tmt) REVERT: A 743 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7773 (mpt) REVERT: A 804 ILE cc_start: 0.9131 (mt) cc_final: 0.8851 (mp) REVERT: A 891 ASN cc_start: 0.8333 (m-40) cc_final: 0.7383 (t0) REVERT: A 974 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6686 (ppp) outliers start: 20 outliers final: 12 residues processed: 82 average time/residue: 1.0837 time to fit residues: 98.7647 Evaluate side-chains 78 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11724 Z= 0.189 Angle : 0.535 12.659 15896 Z= 0.270 Chirality : 0.042 0.168 1829 Planarity : 0.003 0.042 1978 Dihedral : 8.816 141.048 1759 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.45 % Allowed : 17.60 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1397 helix: -0.45 (0.22), residues: 591 sheet: -0.49 (0.35), residues: 213 loop : -0.78 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 111 HIS 0.003 0.001 HIS A1198 PHE 0.017 0.001 PHE A1103 TYR 0.025 0.001 TYR A 776 ARG 0.002 0.000 ARG A 838 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2794 Ramachandran restraints generated. 1397 Oldfield, 0 Emsley, 1397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 570 MET cc_start: 0.7981 (mtp) cc_final: 0.7652 (mtp) REVERT: A 705 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6224 (tmt) REVERT: A 743 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7776 (mpt) REVERT: A 804 ILE cc_start: 0.9136 (mt) cc_final: 0.8832 (mp) REVERT: A 891 ASN cc_start: 0.8338 (m-40) cc_final: 0.7392 (t0) REVERT: A 974 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6706 (ppp) REVERT: C 186 ILE cc_start: 0.8787 (mp) cc_final: 0.8548 (tt) outliers start: 18 outliers final: 12 residues processed: 78 average time/residue: 1.0015 time to fit residues: 87.8034 Evaluate side-chains 76 residues out of total 1244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 20 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 649 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.117295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.080320 restraints weight = 18262.632| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.47 r_work: 0.3032 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11724 Z= 0.202 Angle : 0.545 12.616 15896 Z= 0.275 Chirality : 0.043 0.168 1829 Planarity : 0.004 0.042 1978 Dihedral : 8.790 140.245 1759 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.45 % Allowed : 17.85 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1397 helix: -0.48 (0.22), residues: 602 sheet: -0.54 (0.35), residues: 215 loop : -0.74 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 772 HIS 0.003 0.001 HIS A1198 PHE 0.015 0.001 PHE A1103 TYR 0.031 0.001 TYR A 776 ARG 0.002 0.000 ARG A 838 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3253.41 seconds wall clock time: 59 minutes 36.15 seconds (3576.15 seconds total)