Starting phenix.real_space_refine (version: dev) on Mon Apr 4 17:14:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/04_2022/6pz9_20528_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/04_2022/6pz9_20528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/04_2022/6pz9_20528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/04_2022/6pz9_20528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/04_2022/6pz9_20528_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/04_2022/6pz9_20528_neut_updated.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 486": "NH1" <-> "NH2" Residue "C ARG 598": "NH1" <-> "NH2" Residue "C ARG 702": "NH1" <-> "NH2" Residue "C ARG 837": "NH1" <-> "NH2" Residue "C ARG 1300": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7773 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 7612 Classifications: {'peptide': 1177} Incomplete info: {'truncation_to_alanine': 512} Link IDs: {'PTRANS': 37, 'TRANS': 1139} Chain breaks: 6 Unresolved non-hydrogen bonds: 1666 Unresolved non-hydrogen angles: 2111 Unresolved non-hydrogen dihedrals: 1298 Unresolved non-hydrogen chiralities: 217 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 22, 'TRP:plan': 3, 'ASP:plan': 39, 'PHE:plan': 17, 'GLU:plan': 37, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 778 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 97 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'ATP': 1, 'BJX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BJX C1601 " occ=0.00 ... (31 atoms not shown) pdb=" O3 BJX C1601 " occ=0.00 Time building chain proxies: 5.39, per 1000 atoms: 0.69 Number of scatterers: 7773 At special positions: 0 Unit cell: (97.185, 85.69, 131.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 3 15.00 O 1393 8.00 N 1411 7.00 C 4940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 6 sheets defined 62.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 231 through 242 removed outlier: 3.810A pdb=" N ALA C 235 " --> pdb=" O TRP C 232 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE C 237 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS C 238 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 239 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 240 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 241 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 276 Processing helix chain 'C' and resid 284 through 325 removed outlier: 5.870A pdb=" N ARG C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Proline residue: C 317 - end of helix Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 356 through 401 removed outlier: 3.540A pdb=" N VAL C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 411 No H-bonds generated for 'chain 'C' and resid 408 through 411' Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 423 through 433 removed outlier: 3.715A pdb=" N PHE C 431 " --> pdb=" O GLN C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 455 removed outlier: 3.883A pdb=" N TRP C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) Proline residue: C 442 - end of helix Processing helix chain 'C' and resid 458 through 468 removed outlier: 3.508A pdb=" N VAL C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 504 removed outlier: 3.644A pdb=" N VAL C 477 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 482 " --> pdb=" O ALA C 478 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 515 through 540 removed outlier: 3.696A pdb=" N VAL C 524 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 525 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 535 " --> pdb=" O THR C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 564 Proline residue: C 551 - end of helix Processing helix chain 'C' and resid 573 through 613 removed outlier: 3.988A pdb=" N ALA C 578 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 581 " --> pdb=" O PHE C 577 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR C 588 " --> pdb=" O HIS C 584 " (cutoff:3.500A) Proline residue: C 589 - end of helix removed outlier: 3.896A pdb=" N SER C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 599 " --> pdb=" O SER C 595 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 603 " --> pdb=" O SER C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 726 removed outlier: 3.562A pdb=" N LEU C 723 " --> pdb=" O LYS C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 789 Processing helix chain 'C' and resid 796 through 805 Processing helix chain 'C' and resid 808 through 814 Processing helix chain 'C' and resid 818 through 820 No H-bonds generated for 'chain 'C' and resid 818 through 820' Processing helix chain 'C' and resid 832 through 845 removed outlier: 3.722A pdb=" N ALA C 843 " --> pdb=" O SER C 839 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 844 " --> pdb=" O VAL C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 880 removed outlier: 3.605A pdb=" N GLU C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 918 Processing helix chain 'C' and resid 923 through 927 Processing helix chain 'C' and resid 997 through 1007 removed outlier: 4.086A pdb=" N SER C1006 " --> pdb=" O THR C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1038 removed outlier: 4.704A pdb=" N LEU C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C1021 " --> pdb=" O VAL C1017 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL C1028 " --> pdb=" O HIS C1024 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP C1031 " --> pdb=" O LEU C1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C1038 " --> pdb=" O LEU C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1062 through 1103 removed outlier: 3.516A pdb=" N LEU C1070 " --> pdb=" O MET C1066 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU C1074 " --> pdb=" O LEU C1070 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C1087 " --> pdb=" O SER C1083 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG C1096 " --> pdb=" O LYS C1092 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER C1100 " --> pdb=" O ARG C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1115 Processing helix chain 'C' and resid 1118 through 1134 removed outlier: 3.765A pdb=" N ASP C1128 " --> pdb=" O ARG C1124 " (cutoff:3.500A) Processing helix chain 'C' and resid 1136 through 1160 removed outlier: 4.064A pdb=" N LEU C1148 " --> pdb=" O SER C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1209 Proline residue: C1170 - end of helix removed outlier: 3.650A pdb=" N VAL C1173 " --> pdb=" O LEU C1169 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C1184 " --> pdb=" O LYS C1180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C1185 " --> pdb=" O TYR C1181 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP C1188 " --> pdb=" O VAL C1184 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C1198 " --> pdb=" O ASP C1194 " (cutoff:3.500A) Proline residue: C1199 - end of helix removed outlier: 4.117A pdb=" N VAL C1208 " --> pdb=" O PHE C1204 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1216 Processing helix chain 'C' and resid 1220 through 1271 removed outlier: 4.075A pdb=" N GLN C1225 " --> pdb=" O ALA C1221 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C1226 " --> pdb=" O ARG C1222 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C1227 " --> pdb=" O PHE C1223 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C1232 " --> pdb=" O LEU C1228 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C1236 " --> pdb=" O ASP C1232 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C1237 " --> pdb=" O SER C1233 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C1240 " --> pdb=" O ILE C1236 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C1241 " --> pdb=" O ALA C1237 " (cutoff:3.500A) Processing helix chain 'C' and resid 1281 through 1293 removed outlier: 3.945A pdb=" N LEU C1289 " --> pdb=" O LEU C1285 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER C1292 " --> pdb=" O ALA C1288 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN C1293 " --> pdb=" O LEU C1289 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1320 removed outlier: 3.948A pdb=" N ALA C1311 " --> pdb=" O ILE C1307 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL C1312 " --> pdb=" O GLN C1308 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C1313 " --> pdb=" O LEU C1309 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C1314 " --> pdb=" O GLY C1310 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE C1315 " --> pdb=" O ALA C1311 " (cutoff:3.500A) Processing helix chain 'C' and resid 1385 through 1393 removed outlier: 3.583A pdb=" N PHE C1392 " --> pdb=" O PHE C1388 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE C1393 " --> pdb=" O SER C1389 " (cutoff:3.500A) Processing helix chain 'C' and resid 1410 through 1412 No H-bonds generated for 'chain 'C' and resid 1410 through 1412' Processing helix chain 'C' and resid 1415 through 1421 Processing helix chain 'C' and resid 1436 through 1440 Processing helix chain 'C' and resid 1449 through 1458 removed outlier: 3.748A pdb=" N ALA C1458 " --> pdb=" O ALA C1454 " (cutoff:3.500A) Processing helix chain 'C' and resid 1461 through 1465 Processing helix chain 'C' and resid 1485 through 1498 Processing helix chain 'C' and resid 1513 through 1530 Processing helix chain 'C' and resid 1566 through 1569 No H-bonds generated for 'chain 'C' and resid 1566 through 1569' Processing helix chain 'C' and resid 1571 through 1577 Processing sheet with id= A, first strand: chain 'C' and resid 709 through 711 removed outlier: 6.272A pdb=" N ALA C 771 " --> pdb=" O PHE C 852 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASP C 854 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA C 773 " --> pdb=" O ASP C 854 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 1402 through 1404 removed outlier: 3.649A pdb=" N THR C1367 " --> pdb=" O ILE C1347 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL C1365 " --> pdb=" O ASN C1349 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 1423 through 1425 removed outlier: 3.904A pdb=" N ILE C1425 " --> pdb=" O ILE C1504 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 685 through 687 removed outlier: 7.148A pdb=" N THR C 687 " --> pdb=" O LYS C 732 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS C 732 " --> pdb=" O THR C 687 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 901 through 904 removed outlier: 5.343A pdb=" N LYS C 904 " --> pdb=" O ILE C 908 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE C 908 " --> pdb=" O LYS C 904 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 1549 through 1552 481 hydrogen bonds defined for protein. 1419 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: 2.44 Time building geometry restraints manager: 3.59 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: 1273 1.31 - 1.43: 2104 1.43 - 1.56: 4499 1.56 - 1.69: 5 1.69 - 1.81: 40 Bond restraints: 7921 Sorted by residual: bond pdb=" C4 ATP C1602 " pdb=" C5 ATP C1602 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.63e+01 bond pdb=" C5 ATP C1602 " pdb=" C6 ATP C1602 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.50e+01 bond pdb=" C4 ATP C1602 " pdb=" N9 ATP C1602 " ideal model delta sigma weight residual 1.374 1.316 0.058 1.00e-02 1.00e+04 3.42e+01 bond pdb=" C16 BJX C1601 " pdb=" N1 BJX C1601 " ideal model delta sigma weight residual 1.344 1.448 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C5 ATP C1602 " pdb=" N7 ATP C1602 " ideal model delta sigma weight residual 1.387 1.336 0.051 1.00e-02 1.00e+04 2.56e+01 ... (remaining 7916 not shown) Histogram of bond angle deviations from ideal: 96.33 - 104.30: 107 104.30 - 112.27: 4004 112.27 - 120.24: 3459 120.24 - 128.22: 3247 128.22 - 136.19: 80 Bond angle restraints: 10897 Sorted by residual: angle pdb=" PA ATP C1602 " pdb=" O3A ATP C1602 " pdb=" PB ATP C1602 " ideal model delta sigma weight residual 136.83 116.72 20.11 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB ATP C1602 " pdb=" O3B ATP C1602 " pdb=" PG ATP C1602 " ideal model delta sigma weight residual 139.87 120.87 19.00 1.00e+00 1.00e+00 3.61e+02 angle pdb=" N LYS D 5 " pdb=" CA LYS D 5 " pdb=" C LYS D 5 " ideal model delta sigma weight residual 110.88 101.94 8.94 1.28e+00 6.10e-01 4.88e+01 angle pdb=" C5 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N3 ATP C1602 " ideal model delta sigma weight residual 126.80 120.16 6.64 1.00e+00 1.00e+00 4.41e+01 angle pdb=" N3 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N9 ATP C1602 " ideal model delta sigma weight residual 127.04 133.58 -6.54 1.15e+00 7.59e-01 3.25e+01 ... (remaining 10892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.81: 4534 30.81 - 61.63: 40 61.63 - 92.44: 10 92.44 - 123.25: 3 123.25 - 154.06: 1 Dihedral angle restraints: 4588 sinusoidal: 1106 harmonic: 3482 Sorted by residual: dihedral pdb=" CA SER C 280 " pdb=" C SER C 280 " pdb=" N PRO C 281 " pdb=" CA PRO C 281 " ideal model delta harmonic sigma weight residual -180.00 -146.85 -33.15 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA ALA C1331 " pdb=" C ALA C1331 " pdb=" N PRO C1332 " pdb=" CA PRO C1332 " ideal model delta harmonic sigma weight residual 180.00 -148.46 -31.54 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA PHE C1528 " pdb=" C PHE C1528 " pdb=" N ALA C1529 " pdb=" CA ALA C1529 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 4585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 969 0.065 - 0.130: 311 0.130 - 0.195: 47 0.195 - 0.260: 4 0.260 - 0.325: 5 Chirality restraints: 1336 Sorted by residual: chirality pdb=" CG LEU C1248 " pdb=" CB LEU C1248 " pdb=" CD1 LEU C1248 " pdb=" CD2 LEU C1248 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C5 BJX C1601 " pdb=" C7 BJX C1601 " pdb=" C8 BJX C1601 " pdb=" N1 BJX C1601 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE C1255 " pdb=" CA ILE C1255 " pdb=" CG1 ILE C1255 " pdb=" CG2 ILE C1255 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1333 not shown) Planarity restraints: 1419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C1037 " -0.028 2.00e-02 2.50e+03 2.90e-02 2.10e+01 pdb=" CG TRP C1037 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP C1037 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP C1037 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1037 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C1037 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1037 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1037 " -0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP C1037 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 243 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO C 244 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 244 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 244 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 316 " -0.055 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO C 317 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 317 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 317 " -0.045 5.00e-02 4.00e+02 ... (remaining 1416 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 892 2.74 - 3.28: 7962 3.28 - 3.82: 12520 3.82 - 4.36: 13775 4.36 - 4.90: 23344 Nonbonded interactions: 58493 Sorted by model distance: nonbonded pdb=" OG1 THR C 371 " pdb=" OH TYR C1254 " model vdw 2.205 2.440 nonbonded pdb=" N ASN C 781 " pdb=" OE2 GLU C1206 " model vdw 2.227 2.520 nonbonded pdb=" O SER C 302 " pdb=" OG SER C 376 " model vdw 2.249 2.440 nonbonded pdb=" O LEU C1192 " pdb=" OG1 THR C1196 " model vdw 2.256 2.440 nonbonded pdb=" O THR C1161 " pdb=" OG1 THR C1161 " model vdw 2.262 2.440 ... (remaining 58488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 26 5.16 5 C 4940 2.51 5 N 1411 2.21 5 O 1393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 1.420 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 24.980 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 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 : 0.009 0.104 7921 Z= 0.595 Angle : 1.214 20.108 10897 Z= 0.709 Chirality : 0.064 0.325 1336 Planarity : 0.009 0.084 1419 Dihedral : 12.292 154.064 2318 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.09 % 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: -3.88 (0.20), residues: 1180 helix: -2.02 (0.15), residues: 763 sheet: -2.96 (0.59), residues: 67 loop : -3.38 (0.27), residues: 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.990 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1713 time to fit residues: 43.5948 Evaluate side-chains 125 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 ASN C 273 GLN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 HIS C 707 GLN C 896 HIS C1098 HIS C1316 HIS C1364 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 7921 Z= 0.180 Angle : 0.634 10.193 10897 Z= 0.326 Chirality : 0.043 0.296 1336 Planarity : 0.006 0.084 1419 Dihedral : 8.502 160.517 1260 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.23), residues: 1180 helix: -0.60 (0.17), residues: 786 sheet: -2.29 (0.64), residues: 57 loop : -3.09 (0.29), residues: 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.944 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 161 average time/residue: 0.1413 time to fit residues: 34.3307 Evaluate side-chains 125 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0708 time to fit residues: 2.6610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 50.0000 chunk 33 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 50.0000 chunk 115 optimal weight: 20.0000 chunk 95 optimal weight: 0.0010 chunk 106 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 86 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: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 867 HIS C1197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.962 7921 Z= 0.903 Angle : 1.247 106.100 10897 Z= 0.496 Chirality : 0.044 0.298 1336 Planarity : 0.005 0.081 1419 Dihedral : 8.296 161.656 1260 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.09 % 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: -1.76 (0.23), residues: 1180 helix: -0.28 (0.18), residues: 785 sheet: -2.24 (0.64), residues: 57 loop : -2.96 (0.29), residues: 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.871 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 133 average time/residue: 0.1355 time to fit residues: 27.6067 Evaluate side-chains 118 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0718 time to fit residues: 2.1671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 50.0000 chunk 72 optimal weight: 7.9990 chunk 107 optimal weight: 50.0000 chunk 114 optimal weight: 40.0000 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 0.0270 chunk 30 optimal weight: 0.2980 overall best weight: 2.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 7921 Z= 0.208 Angle : 0.605 9.796 10897 Z= 0.306 Chirality : 0.043 0.253 1336 Planarity : 0.005 0.099 1419 Dihedral : 8.051 165.140 1260 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 2.55 % 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: -1.12 (0.24), residues: 1180 helix: 0.25 (0.18), residues: 783 sheet: -2.46 (0.60), residues: 69 loop : -2.67 (0.30), residues: 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 137 average time/residue: 0.1411 time to fit residues: 28.9355 Evaluate side-chains 115 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0746 time to fit residues: 2.2307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 102 optimal weight: 0.0470 chunk 28 optimal weight: 5.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 ASN ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.127 7921 Z= 0.212 Angle : 0.595 9.802 10897 Z= 0.299 Chirality : 0.043 0.245 1336 Planarity : 0.004 0.096 1419 Dihedral : 7.885 167.281 1260 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 2.36 % 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: -0.68 (0.24), residues: 1180 helix: 0.57 (0.19), residues: 787 sheet: -2.04 (0.67), residues: 62 loop : -2.57 (0.31), residues: 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.933 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 0.1290 time to fit residues: 27.3506 Evaluate side-chains 122 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0759 time to fit residues: 2.4257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 114 optimal weight: 0.3980 chunk 94 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 30.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.854 7921 Z= 0.861 Angle : 1.285 106.098 10897 Z= 0.525 Chirality : 0.045 0.318 1336 Planarity : 0.005 0.108 1419 Dihedral : 7.890 167.303 1260 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1180 helix: 0.55 (0.19), residues: 787 sheet: -2.03 (0.67), residues: 62 loop : -2.56 (0.31), residues: 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.938 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1341 time to fit residues: 24.2520 Evaluate side-chains 112 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 40.0000 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 113 optimal weight: 40.0000 chunk 71 optimal weight: 0.3980 chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.854 7921 Z= 0.872 Angle : 1.299 106.100 10897 Z= 0.546 Chirality : 0.045 0.318 1336 Planarity : 0.006 0.108 1419 Dihedral : 7.890 167.303 1260 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1180 helix: 0.55 (0.19), residues: 787 sheet: -2.03 (0.67), residues: 62 loop : -2.56 (0.31), residues: 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.921 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1276 time to fit residues: 22.3522 Evaluate side-chains 112 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 0.0770 chunk 89 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.854 7921 Z= 0.872 Angle : 1.299 106.100 10897 Z= 0.546 Chirality : 0.045 0.318 1336 Planarity : 0.006 0.108 1419 Dihedral : 7.890 167.303 1260 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1180 helix: 0.55 (0.19), residues: 787 sheet: -2.03 (0.67), residues: 62 loop : -2.56 (0.31), residues: 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.973 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1354 time to fit residues: 23.6434 Evaluate side-chains 112 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 100 optimal weight: 40.0000 chunk 69 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.854 7921 Z= 0.872 Angle : 1.299 106.100 10897 Z= 0.546 Chirality : 0.045 0.318 1336 Planarity : 0.006 0.108 1419 Dihedral : 7.890 167.303 1260 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1180 helix: 0.55 (0.19), residues: 787 sheet: -2.03 (0.67), residues: 62 loop : -2.56 (0.31), residues: 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.966 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1339 time to fit residues: 23.3446 Evaluate side-chains 112 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 0.0970 chunk 57 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 99 optimal weight: 0.2980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.854 7921 Z= 0.872 Angle : 1.299 106.100 10897 Z= 0.546 Chirality : 0.045 0.318 1336 Planarity : 0.006 0.108 1419 Dihedral : 7.890 167.303 1260 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1180 helix: 0.55 (0.19), residues: 787 sheet: -2.03 (0.67), residues: 62 loop : -2.56 (0.31), residues: 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.946 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1337 time to fit residues: 23.3166 Evaluate side-chains 112 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 93 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1203 HIS ** 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 = 0.4194 r_free = 0.4194 target = 0.161291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.142295 restraints weight = 14446.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.145573 restraints weight = 6640.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.147601 restraints weight = 3777.649| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.854 7921 Z= 0.872 Angle : 1.299 106.100 10897 Z= 0.546 Chirality : 0.045 0.318 1336 Planarity : 0.006 0.108 1419 Dihedral : 7.890 167.303 1260 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1180 helix: 0.55 (0.19), residues: 787 sheet: -2.03 (0.67), residues: 62 loop : -2.56 (0.31), residues: 331 =============================================================================== Job complete usr+sys time: 1342.85 seconds wall clock time: 25 minutes 9.99 seconds (1509.99 seconds total)