Starting phenix.real_space_refine on Sun Apr 7 00:27:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbx_21600/04_2024/6wbx_21600.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbx_21600/04_2024/6wbx_21600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbx_21600/04_2024/6wbx_21600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbx_21600/04_2024/6wbx_21600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbx_21600/04_2024/6wbx_21600.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbx_21600/04_2024/6wbx_21600.pdb" } resolution = 3.5 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 18 5.16 5 C 5829 2.51 5 N 1629 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 645": "OD1" <-> "OD2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "A ARG 671": "NH1" <-> "NH2" Residue "A ASP 673": "OD1" <-> "OD2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ASP 694": "OD1" <-> "OD2" Residue "A ASP 720": "OD1" <-> "OD2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A ASP 761": "OD1" <-> "OD2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A ASP 827": "OD1" <-> "OD2" Residue "A TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 911": "NH1" <-> "NH2" Residue "A ARG 924": "NH1" <-> "NH2" Residue "A ARG 936": "NH1" <-> "NH2" Residue "A ASP 937": "OD1" <-> "OD2" Residue "A ASP 955": "OD1" <-> "OD2" Residue "A ASP 977": "OD1" <-> "OD2" Residue "A ARG 1027": "NH1" <-> "NH2" Residue "A ASP 1030": "OD1" <-> "OD2" Residue "A ASP 1091": "OD1" <-> "OD2" Residue "A ASP 1152": "OD1" <-> "OD2" Residue "A ASP 1191": "OD1" <-> "OD2" Residue "A ARG 1204": "NH1" <-> "NH2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "A ASP 1220": "OD1" <-> "OD2" Residue "A PHE 1252": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9170 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1266, 9160 Unusual residues: {' CA': 2} Classifications: {'peptide': 1264, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 103, 'TRANS': 1159, None: 2} Not linked: pdbres="VAL A1388 " pdbres=" CA A2001 " Not linked: pdbres=" CA A2001 " pdbres=" CA A2002 " Chain breaks: 9 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 153 Conformer: "B" Number of residues, atoms: 1266, 9160 Unusual residues: {' CA': 2} Classifications: {'peptide': 1264, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 103, 'TRANS': 1159, None: 2} Not linked: pdbres="VAL A1388 " pdbres=" CA A2001 " Not linked: pdbres=" CA A2001 " pdbres=" CA A2002 " Chain breaks: 9 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 153 bond proxies already assigned to first conformer: 9366 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 550 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 550 " occ=0.50 Time building chain proxies: 9.40, per 1000 atoms: 1.03 Number of scatterers: 9170 At special positions: 0 Unit cell: (131.502, 88.0215, 90.1425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 18 16.00 O 1692 8.00 N 1629 7.00 C 5829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 895 " distance=2.02 Simple disulfide: pdb=" SG CYS A1104 " - pdb=" SG CYS A1139 " 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: 3.35 Conformation dependent library (CDL) restraints added in 3.5 seconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 16 sheets defined 31.0% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 11 through 13 No H-bonds generated for 'chain 'A' and resid 11 through 13' Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.957A pdb=" N ALA A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.604A pdb=" N ALA A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.832A pdb=" N PHE A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.521A pdb=" N LEU A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.739A pdb=" N GLN A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 112 " --> pdb=" O TRP A 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.839A pdb=" N ILE A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 154 through 165 removed outlier: 3.759A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 173 through 185 removed outlier: 4.204A pdb=" N SER A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 removed outlier: 3.525A pdb=" N CYS A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 207 Processing helix chain 'A' and resid 211 through 229 removed outlier: 3.712A pdb=" N PHE A 217 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 219 " --> pdb=" O TRP A 215 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 3.640A pdb=" N ALA A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 243 removed outlier: 3.877A pdb=" N PHE A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 309 removed outlier: 4.060A pdb=" N ALA A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 331 removed outlier: 3.706A pdb=" N VAL A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 363 through 381 removed outlier: 3.760A pdb=" N LEU A 368 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.706A pdb=" N LEU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG A 380 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.972A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.199A pdb=" N ALA A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.577A pdb=" N GLN A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.525A pdb=" N AHIS A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 551 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 620 through 629 removed outlier: 4.544A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 732 removed outlier: 3.814A pdb=" N SER A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 939 removed outlier: 4.239A pdb=" N LEU A 938 " --> pdb=" O GLN A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 964 removed outlier: 3.584A pdb=" N ALA A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1103 through 1107 removed outlier: 3.566A pdb=" N GLY A1107 " --> pdb=" O CYS A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1130 removed outlier: 4.120A pdb=" N ASP A1130 " --> pdb=" O ARG A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1268 through 1276 removed outlier: 3.547A pdb=" N ALA A1276 " --> pdb=" O LEU A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1308 removed outlier: 3.687A pdb=" N ALA A1304 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1353 removed outlier: 3.609A pdb=" N GLY A1344 " --> pdb=" O VAL A1340 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A1349 " --> pdb=" O GLY A1345 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A1350 " --> pdb=" O SER A1346 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A1353 " --> pdb=" O LEU A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1388 removed outlier: 3.526A pdb=" N ALA A1376 " --> pdb=" O ILE A1372 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A1382 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A1383 " --> pdb=" O SER A1379 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A1384 " --> pdb=" O VAL A1380 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A1385 " --> pdb=" O ALA A1381 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 455 through 459 removed outlier: 5.635A pdb=" N ARG A 455 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 457 " --> pdb=" O TYR A 529 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA A 594 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS A 561 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 577 through 579 removed outlier: 6.865A pdb=" N VAL A 578 " --> pdb=" O ARG A1061 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1181 through 1182 removed outlier: 3.623A pdb=" N GLN A1236 " --> pdb=" O VAL A1208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 642 removed outlier: 7.539A pdb=" N ARG A 614 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR A 659 " --> pdb=" O ARG A 614 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 873 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL A1163 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG A 928 " --> pdb=" O VAL A1163 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A1169 " --> pdb=" O THR A 922 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AA7, first strand: chain 'A' and resid 710 through 714 removed outlier: 7.193A pdb=" N THR A 817 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ARG A 764 " --> pdb=" O GLU A 815 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N GLU A 815 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 745 through 746 removed outlier: 6.760A pdb=" N THR A 774 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU A 840 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 772 " --> pdb=" O LEU A 840 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 843 through 844 Processing sheet with id=AB1, first strand: chain 'A' and resid 886 through 887 Processing sheet with id=AB2, first strand: chain 'A' and resid 909 through 915 Processing sheet with id=AB3, first strand: chain 'A' and resid 947 through 949 removed outlier: 6.713A pdb=" N VAL A1050 " --> pdb=" O ILE A1018 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE A1018 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A1052 " --> pdb=" O VAL A1016 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A1016 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP A1054 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 999 through 1002 removed outlier: 3.628A pdb=" N LEU A1002 " --> pdb=" O THR A1036 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1099 through 1102 Processing sheet with id=AB6, first strand: chain 'A' and resid 1099 through 1102 Processing sheet with id=AB7, first strand: chain 'A' and resid 1195 through 1197 removed outlier: 3.748A pdb=" N GLY A1246 " --> pdb=" O ALA A1197 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A1251 " --> pdb=" O ALA A1217 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 732 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: 3.41 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2999 1.34 - 1.45: 1551 1.45 - 1.57: 4812 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 9390 Sorted by residual: bond pdb=" CB VAL A 703 " pdb=" CG2 VAL A 703 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.52e+00 bond pdb=" CB VAL A1229 " pdb=" CG2 VAL A1229 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.65e+00 bond pdb=" CB VAL A1009 " pdb=" CG2 VAL A1009 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.26e+00 bond pdb=" C LYS A 993 " pdb=" N PRO A 994 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.79e+00 bond pdb=" CG LEU A 162 " pdb=" CD2 LEU A 162 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.64e+00 ... (remaining 9385 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.51: 453 106.51 - 113.47: 5302 113.47 - 120.44: 3645 120.44 - 127.41: 3345 127.41 - 134.37: 165 Bond angle restraints: 12910 Sorted by residual: angle pdb=" N THR A 661 " pdb=" CA THR A 661 " pdb=" C THR A 661 " ideal model delta sigma weight residual 109.81 120.37 -10.56 2.21e+00 2.05e-01 2.28e+01 angle pdb=" C LEU A 362 " pdb=" N GLU A 363 " pdb=" CA GLU A 363 " ideal model delta sigma weight residual 120.51 126.61 -6.10 1.45e+00 4.76e-01 1.77e+01 angle pdb=" N PRO A1010 " pdb=" CA PRO A1010 " pdb=" C PRO A1010 " ideal model delta sigma weight residual 112.47 104.76 7.71 2.06e+00 2.36e-01 1.40e+01 angle pdb=" C VAL A 615 " pdb=" N ALA A 616 " pdb=" CA ALA A 616 " ideal model delta sigma weight residual 122.65 116.88 5.77 1.60e+00 3.91e-01 1.30e+01 angle pdb=" N LEU A 724 " pdb=" CA LEU A 724 " pdb=" C LEU A 724 " ideal model delta sigma weight residual 109.81 117.66 -7.85 2.21e+00 2.05e-01 1.26e+01 ... (remaining 12905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5069 17.54 - 35.07: 401 35.07 - 52.60: 77 52.60 - 70.14: 7 70.14 - 87.67: 6 Dihedral angle restraints: 5560 sinusoidal: 1984 harmonic: 3576 Sorted by residual: dihedral pdb=" CA PRO A 355 " pdb=" C PRO A 355 " pdb=" N LEU A 356 " pdb=" CA LEU A 356 " ideal model delta harmonic sigma weight residual 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA PRO A 866 " pdb=" C PRO A 866 " pdb=" N ALA A 867 " pdb=" CA ALA A 867 " ideal model delta harmonic sigma weight residual -180.00 -153.58 -26.42 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PRO A 588 " pdb=" C PRO A 588 " pdb=" N ALA A 589 " pdb=" CA ALA A 589 " ideal model delta harmonic sigma weight residual 180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1289 0.083 - 0.165: 229 0.165 - 0.248: 14 0.248 - 0.331: 3 0.331 - 0.414: 2 Chirality restraints: 1537 Sorted by residual: chirality pdb=" CB VAL A 405 " pdb=" CA VAL A 405 " pdb=" CG1 VAL A 405 " pdb=" CG2 VAL A 405 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA THR A 661 " pdb=" N THR A 661 " pdb=" C THR A 661 " pdb=" CB THR A 661 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB ILE A 491 " pdb=" CA ILE A 491 " pdb=" CG1 ILE A 491 " pdb=" CG2 ILE A 491 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1534 not shown) Planarity restraints: 1681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 61 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 62 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 222 " 0.051 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO A 223 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 35 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO A 36 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.038 5.00e-02 4.00e+02 ... (remaining 1678 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1121 2.73 - 3.27: 8173 3.27 - 3.82: 14406 3.82 - 4.36: 16921 4.36 - 4.90: 30591 Nonbonded interactions: 71212 Sorted by model distance: nonbonded pdb=" O ALA A 962 " pdb="CA CA A2002 " model vdw 2.190 2.510 nonbonded pdb=" O THR A 970 " pdb="CA CA A2002 " model vdw 2.243 2.510 nonbonded pdb=" OG SER A 715 " pdb=" OE1 GLN A 756 " model vdw 2.268 2.440 nonbonded pdb=" O ASP A 967 " pdb="CA CA A2002 " model vdw 2.281 2.510 nonbonded pdb=" O GLY A 617 " pdb=" OG1 THR A 661 " model vdw 2.283 2.440 ... (remaining 71207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.310 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.012 0.084 9390 Z= 0.785 Angle : 1.069 10.559 12910 Z= 0.578 Chirality : 0.063 0.414 1537 Planarity : 0.010 0.080 1681 Dihedral : 13.487 87.672 3246 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.88 % Favored : 92.04 % Rotamer: Outliers : 0.11 % Allowed : 7.91 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -5.51 (0.17), residues: 1247 helix: -5.01 (0.08), residues: 363 sheet: -2.68 (0.32), residues: 208 loop : -3.23 (0.18), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 221 HIS 0.010 0.002 HIS A 675 PHE 0.028 0.003 PHE A 433 TYR 0.018 0.003 TYR A1258 ARG 0.011 0.001 ARG A1219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.952 Fit side-chains REVERT: A 673 ASP cc_start: 0.7801 (p0) cc_final: 0.7579 (p0) REVERT: A 1099 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8681 (tttp) REVERT: A 1119 MET cc_start: 0.8999 (mtt) cc_final: 0.8666 (mtt) outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.2794 time to fit residues: 33.1840 Evaluate side-chains 59 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1036 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 114 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 29 GLN ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 551 HIS A 675 HIS ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9390 Z= 0.215 Angle : 0.622 11.397 12910 Z= 0.308 Chirality : 0.043 0.172 1537 Planarity : 0.007 0.065 1681 Dihedral : 5.374 21.794 1340 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.21 % Allowed : 11.32 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -4.46 (0.19), residues: 1247 helix: -3.83 (0.16), residues: 378 sheet: -2.11 (0.34), residues: 206 loop : -2.70 (0.20), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 205 HIS 0.003 0.001 HIS A 675 PHE 0.011 0.002 PHE A 246 TYR 0.012 0.001 TYR A 593 ARG 0.006 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 1.015 Fit side-chains REVERT: A 648 GLN cc_start: 0.8311 (tp-100) cc_final: 0.8035 (tt0) REVERT: A 1119 MET cc_start: 0.8886 (mtt) cc_final: 0.8534 (mtt) outliers start: 11 outliers final: 7 residues processed: 77 average time/residue: 0.2130 time to fit residues: 23.7308 Evaluate side-chains 65 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 0.0010 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9390 Z= 0.215 Angle : 0.579 8.737 12910 Z= 0.282 Chirality : 0.043 0.154 1537 Planarity : 0.006 0.058 1681 Dihedral : 4.828 26.458 1340 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.43 % Allowed : 12.20 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -3.55 (0.21), residues: 1247 helix: -2.74 (0.21), residues: 379 sheet: -1.84 (0.36), residues: 198 loop : -2.27 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.010 0.001 PHE A 246 TYR 0.011 0.001 TYR A 593 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.992 Fit side-chains REVERT: A 648 GLN cc_start: 0.8287 (tp-100) cc_final: 0.8028 (tt0) REVERT: A 1119 MET cc_start: 0.8867 (mtt) cc_final: 0.8484 (mtt) outliers start: 13 outliers final: 11 residues processed: 78 average time/residue: 0.2209 time to fit residues: 24.9261 Evaluate side-chains 68 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1154 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9390 Z= 0.180 Angle : 0.548 7.831 12910 Z= 0.264 Chirality : 0.042 0.156 1537 Planarity : 0.005 0.053 1681 Dihedral : 4.558 28.498 1340 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.43 % Allowed : 13.85 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -2.99 (0.22), residues: 1247 helix: -2.08 (0.23), residues: 386 sheet: -1.76 (0.36), residues: 199 loop : -1.96 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.009 0.001 PHE A 217 TYR 0.011 0.001 TYR A 593 ARG 0.004 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 1.078 Fit side-chains REVERT: A 152 MET cc_start: 0.7921 (tmm) cc_final: 0.7450 (tpp) REVERT: A 421 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 1119 MET cc_start: 0.8873 (mtt) cc_final: 0.8518 (mtt) outliers start: 13 outliers final: 12 residues processed: 77 average time/residue: 0.2243 time to fit residues: 25.0319 Evaluate side-chains 73 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1248 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.0670 chunk 69 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9390 Z= 0.211 Angle : 0.561 7.816 12910 Z= 0.269 Chirality : 0.043 0.205 1537 Planarity : 0.005 0.050 1681 Dihedral : 4.486 29.728 1340 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.20 % Allowed : 14.62 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -2.68 (0.22), residues: 1247 helix: -1.65 (0.25), residues: 386 sheet: -1.73 (0.36), residues: 199 loop : -1.84 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.009 0.001 PHE A 689 TYR 0.010 0.001 TYR A 593 ARG 0.004 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 1.073 Fit side-chains REVERT: A 304 MET cc_start: 0.8258 (mmm) cc_final: 0.7883 (tmm) REVERT: A 421 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7994 (tp) REVERT: A 1119 MET cc_start: 0.8887 (mtt) cc_final: 0.8540 (mtt) outliers start: 20 outliers final: 16 residues processed: 74 average time/residue: 0.2204 time to fit residues: 23.6565 Evaluate side-chains 77 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1248 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9390 Z= 0.203 Angle : 0.552 7.371 12910 Z= 0.265 Chirality : 0.043 0.162 1537 Planarity : 0.005 0.054 1681 Dihedral : 4.366 29.880 1340 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.98 % Allowed : 15.38 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -2.45 (0.23), residues: 1247 helix: -1.30 (0.26), residues: 386 sheet: -1.58 (0.35), residues: 206 loop : -1.82 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.009 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.004 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 1.008 Fit side-chains REVERT: A 304 MET cc_start: 0.8272 (mmm) cc_final: 0.7870 (tmm) REVERT: A 421 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7968 (tp) REVERT: A 1119 MET cc_start: 0.8911 (mtt) cc_final: 0.8564 (mtt) outliers start: 18 outliers final: 15 residues processed: 74 average time/residue: 0.2323 time to fit residues: 24.8736 Evaluate side-chains 74 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1248 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 0.0470 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9390 Z= 0.229 Angle : 0.561 7.197 12910 Z= 0.270 Chirality : 0.044 0.184 1537 Planarity : 0.005 0.051 1681 Dihedral : 4.395 30.574 1340 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.09 % Allowed : 15.82 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -2.30 (0.23), residues: 1247 helix: -1.05 (0.26), residues: 380 sheet: -1.57 (0.35), residues: 206 loop : -1.77 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.009 0.001 PHE A 689 TYR 0.010 0.001 TYR A 593 ARG 0.003 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.917 Fit side-chains REVERT: A 304 MET cc_start: 0.8263 (mmm) cc_final: 0.7860 (tmm) REVERT: A 421 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8029 (tp) REVERT: A 1119 MET cc_start: 0.8915 (mtt) cc_final: 0.8551 (mtt) REVERT: A 1164 ASP cc_start: 0.8024 (t0) cc_final: 0.7740 (t0) outliers start: 19 outliers final: 15 residues processed: 73 average time/residue: 0.2300 time to fit residues: 24.0830 Evaluate side-chains 73 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1248 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9390 Z= 0.203 Angle : 0.548 7.039 12910 Z= 0.263 Chirality : 0.043 0.169 1537 Planarity : 0.005 0.056 1681 Dihedral : 4.317 30.168 1340 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.87 % Allowed : 16.37 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -2.18 (0.23), residues: 1247 helix: -0.89 (0.27), residues: 388 sheet: -1.54 (0.35), residues: 206 loop : -1.73 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.009 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.003 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.913 Fit side-chains REVERT: A 304 MET cc_start: 0.8247 (mmm) cc_final: 0.7914 (tmm) REVERT: A 421 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8055 (tp) REVERT: A 1119 MET cc_start: 0.8919 (mtt) cc_final: 0.8564 (mtt) REVERT: A 1164 ASP cc_start: 0.7992 (t0) cc_final: 0.7689 (t0) outliers start: 17 outliers final: 14 residues processed: 69 average time/residue: 0.2346 time to fit residues: 23.2294 Evaluate side-chains 72 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1248 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.0030 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 0.0770 chunk 112 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9390 Z= 0.146 Angle : 0.516 7.046 12910 Z= 0.246 Chirality : 0.042 0.146 1537 Planarity : 0.005 0.056 1681 Dihedral : 4.052 28.398 1340 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.54 % Allowed : 16.48 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -1.97 (0.23), residues: 1247 helix: -0.64 (0.27), residues: 390 sheet: -1.42 (0.35), residues: 206 loop : -1.67 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 205 HIS 0.001 0.000 HIS A 551 PHE 0.010 0.001 PHE A 347 TYR 0.010 0.001 TYR A 593 ARG 0.002 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.932 Fit side-chains REVERT: A 152 MET cc_start: 0.7803 (tmm) cc_final: 0.7338 (tpp) REVERT: A 1119 MET cc_start: 0.8889 (mtt) cc_final: 0.8512 (mtt) REVERT: A 1164 ASP cc_start: 0.7906 (t0) cc_final: 0.7626 (t0) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.2279 time to fit residues: 22.4110 Evaluate side-chains 63 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 83 optimal weight: 0.0670 chunk 125 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 79 optimal weight: 0.0370 chunk 106 optimal weight: 2.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9390 Z= 0.144 Angle : 0.513 7.001 12910 Z= 0.244 Chirality : 0.042 0.141 1537 Planarity : 0.005 0.057 1681 Dihedral : 3.921 28.656 1340 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.32 % Allowed : 16.48 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -1.74 (0.23), residues: 1247 helix: -0.40 (0.27), residues: 388 sheet: -1.30 (0.35), residues: 206 loop : -1.55 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 205 HIS 0.001 0.000 HIS A 551 PHE 0.010 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.004 0.000 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.883 Fit side-chains REVERT: A 152 MET cc_start: 0.7792 (tmm) cc_final: 0.7314 (tpp) REVERT: A 1119 MET cc_start: 0.8900 (mtt) cc_final: 0.8522 (mtt) REVERT: A 1164 ASP cc_start: 0.7921 (t0) cc_final: 0.7617 (t0) outliers start: 12 outliers final: 12 residues processed: 66 average time/residue: 0.2371 time to fit residues: 22.1697 Evaluate side-chains 63 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1150 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.087690 restraints weight = 45108.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.090949 restraints weight = 22331.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.091588 restraints weight = 11995.569| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9390 Z= 0.188 Angle : 0.532 6.755 12910 Z= 0.254 Chirality : 0.043 0.144 1537 Planarity : 0.005 0.052 1681 Dihedral : 4.021 29.273 1340 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.32 % Allowed : 16.81 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -1.68 (0.23), residues: 1247 helix: -0.33 (0.27), residues: 388 sheet: -1.26 (0.36), residues: 206 loop : -1.53 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 205 HIS 0.002 0.000 HIS A 551 PHE 0.010 0.001 PHE A 347 TYR 0.011 0.001 TYR A 593 ARG 0.003 0.000 ARG A 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1913.71 seconds wall clock time: 35 minutes 33.08 seconds (2133.08 seconds total)