Starting phenix.real_space_refine on Tue Feb 13 22:07:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/02_2024/6pz9_20528_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/02_2024/6pz9_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_20528/02_2024/6pz9_20528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/02_2024/6pz9_20528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/02_2024/6pz9_20528_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz9_20528/02_2024/6pz9_20528_neut_updated.pdb" } resolution = 3.65 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 ------------------------------------------------------------------------------- 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 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. 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-5238/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: 5.10, per 1000 atoms: 0.66 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 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: 2.39 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: 2.71 Time building geometry restraints manager: 3.51 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: 4555 30.81 - 61.63: 59 61.63 - 92.44: 11 92.44 - 123.25: 3 123.25 - 154.06: 1 Dihedral angle restraints: 4629 sinusoidal: 1147 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 4626 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 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: 0.150 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: 1.030 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.130 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 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 : 12.970 154.064 2359 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.006 TRP C1037 HIS 0.011 0.002 HIS C1098 PHE 0.050 0.005 PHE C 432 TYR 0.040 0.004 TYR C1219 ARG 0.013 0.002 ARG C 388 *********************** 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 : 0.826 Fit side-chains REVERT: C 300 ILE cc_start: 0.8328 (mm) cc_final: 0.8003 (mt) REVERT: C 302 SER cc_start: 0.8600 (p) cc_final: 0.8316 (t) REVERT: C 368 LEU cc_start: 0.9183 (mm) cc_final: 0.8953 (mp) REVERT: C 424 ASP cc_start: 0.8160 (t70) cc_final: 0.7855 (t70) REVERT: C 1154 LEU cc_start: 0.8115 (mm) cc_final: 0.7885 (mt) REVERT: C 1268 ILE cc_start: 0.5943 (mt) cc_final: 0.5678 (mm) REVERT: C 1306 GLU cc_start: 0.7648 (tp30) cc_final: 0.7291 (tp30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1889 time to fit residues: 47.7166 Evaluate side-chains 127 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7921 Z= 0.165 Angle : 0.618 10.085 10897 Z= 0.316 Chirality : 0.043 0.324 1336 Planarity : 0.005 0.061 1419 Dihedral : 10.303 156.580 1301 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.34 % Allowed : 11.79 % Favored : 84.87 % 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: -2.17 (0.23), residues: 1180 helix: -0.60 (0.17), residues: 785 sheet: -2.29 (0.64), residues: 57 loop : -3.09 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C1037 HIS 0.006 0.001 HIS C1098 PHE 0.026 0.002 PHE C 432 TYR 0.016 0.002 TYR C1219 ARG 0.007 0.001 ARG C 486 *********************** 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 163 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: C 262 ASN cc_start: 0.8499 (m110) cc_final: 0.8272 (m-40) REVERT: C 302 SER cc_start: 0.8390 (p) cc_final: 0.8171 (t) REVERT: C 429 MET cc_start: 0.8413 (ttm) cc_final: 0.8154 (ttm) REVERT: C 467 ILE cc_start: 0.7803 (mm) cc_final: 0.7555 (tp) REVERT: C 475 TYR cc_start: 0.8441 (t80) cc_final: 0.8215 (t80) REVERT: C 598 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7782 (ttm110) REVERT: C 867 HIS cc_start: 0.2150 (m90) cc_final: 0.1314 (m170) REVERT: C 889 HIS cc_start: 0.6013 (p90) cc_final: 0.5784 (p-80) REVERT: C 1168 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.6826 (tp) REVERT: C 1190 GLN cc_start: 0.8643 (tp40) cc_final: 0.8339 (mt0) outliers start: 17 outliers final: 10 residues processed: 159 average time/residue: 0.1363 time to fit residues: 32.6677 Evaluate side-chains 135 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1112 PHE Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1168 LEU 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: 8.9990 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 50.0000 chunk 115 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 106 optimal weight: 40.0000 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 GLN C 397 ASN C1273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7921 Z= 0.238 Angle : 0.630 9.858 10897 Z= 0.319 Chirality : 0.045 0.307 1336 Planarity : 0.004 0.049 1419 Dihedral : 9.894 157.294 1301 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.50 % Allowed : 13.75 % Favored : 80.75 % 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: -1.49 (0.24), residues: 1180 helix: -0.06 (0.18), residues: 790 sheet: -2.64 (0.59), residues: 69 loop : -2.81 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C1297 HIS 0.004 0.001 HIS C1024 PHE 0.020 0.002 PHE C 321 TYR 0.015 0.002 TYR C 378 ARG 0.005 0.001 ARG C 486 *********************** 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 168 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 0.928 Fit side-chains REVERT: C 424 ASP cc_start: 0.7988 (t70) cc_final: 0.7639 (t70) REVERT: C 451 LEU cc_start: 0.5503 (pp) cc_final: 0.4929 (mp) REVERT: C 475 TYR cc_start: 0.8553 (t80) cc_final: 0.8352 (t80) REVERT: C 889 HIS cc_start: 0.6091 (p90) cc_final: 0.5890 (p90) REVERT: C 1168 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.6936 (tp) outliers start: 28 outliers final: 21 residues processed: 160 average time/residue: 0.1635 time to fit residues: 38.0842 Evaluate side-chains 143 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 1027 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1112 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1352 VAL 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: 0.8980 chunk 55 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 50.0000 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 50.0000 chunk 114 optimal weight: 50.0000 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7921 Z= 0.272 Angle : 0.654 9.833 10897 Z= 0.330 Chirality : 0.046 0.300 1336 Planarity : 0.004 0.043 1419 Dihedral : 9.649 156.792 1301 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 6.48 % Allowed : 17.09 % Favored : 76.42 % 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: -1.26 (0.24), residues: 1180 helix: 0.14 (0.18), residues: 788 sheet: -2.69 (0.60), residues: 69 loop : -2.73 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C1037 HIS 0.004 0.001 HIS C1364 PHE 0.025 0.002 PHE C 321 TYR 0.016 0.002 TYR C 378 ARG 0.004 0.001 ARG C 598 *********************** 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 160 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: C 424 ASP cc_start: 0.8117 (t70) cc_final: 0.7673 (t70) REVERT: C 451 LEU cc_start: 0.6006 (pp) cc_final: 0.5220 (mt) REVERT: C 598 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7442 (mtp85) REVERT: C 1027 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6975 (mt) REVERT: C 1168 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7070 (tp) REVERT: C 1191 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7842 (mt0) outliers start: 33 outliers final: 25 residues processed: 153 average time/residue: 0.1491 time to fit residues: 33.6278 Evaluate side-chains 147 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1027 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1112 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1161 THR Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7921 Z= 0.173 Angle : 0.570 9.934 10897 Z= 0.285 Chirality : 0.043 0.292 1336 Planarity : 0.004 0.040 1419 Dihedral : 9.250 157.990 1301 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.30 % Allowed : 19.25 % Favored : 75.44 % 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: -0.77 (0.25), residues: 1180 helix: 0.52 (0.19), residues: 784 sheet: -2.71 (0.61), residues: 68 loop : -2.45 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1037 HIS 0.004 0.001 HIS C 863 PHE 0.012 0.001 PHE C 432 TYR 0.012 0.001 TYR C 378 ARG 0.005 0.000 ARG C 265 *********************** 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 151 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: C 386 ASN cc_start: 0.8104 (m-40) cc_final: 0.7893 (m-40) REVERT: C 424 ASP cc_start: 0.8054 (t70) cc_final: 0.7636 (t70) REVERT: C 1027 LEU cc_start: 0.7270 (mt) cc_final: 0.6999 (mt) REVERT: C 1168 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.6951 (tp) REVERT: C 1191 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7900 (mt0) outliers start: 27 outliers final: 22 residues processed: 144 average time/residue: 0.1298 time to fit residues: 28.2815 Evaluate side-chains 143 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 539 TYR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1112 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1296 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 50.0000 chunk 102 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 114 optimal weight: 0.0670 chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 30.0000 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7921 Z= 0.241 Angle : 0.633 9.917 10897 Z= 0.314 Chirality : 0.045 0.273 1336 Planarity : 0.004 0.040 1419 Dihedral : 9.350 158.875 1301 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 6.68 % Allowed : 20.43 % Favored : 72.89 % 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: -0.79 (0.25), residues: 1180 helix: 0.53 (0.19), residues: 780 sheet: -2.79 (0.60), residues: 69 loop : -2.49 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1297 HIS 0.004 0.001 HIS C1364 PHE 0.022 0.002 PHE C 321 TYR 0.020 0.002 TYR C 377 ARG 0.004 0.001 ARG C 265 *********************** 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 155 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 0.891 Fit side-chains REVERT: C 253 LEU cc_start: 0.8149 (tp) cc_final: 0.7647 (tp) REVERT: C 412 MET cc_start: 0.6841 (ptp) cc_final: 0.6345 (ptp) REVERT: C 424 ASP cc_start: 0.8164 (t70) cc_final: 0.7712 (t70) REVERT: C 475 TYR cc_start: 0.8501 (t80) cc_final: 0.7844 (t80) REVERT: C 598 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7803 (mtp85) REVERT: C 1027 LEU cc_start: 0.7250 (mt) cc_final: 0.7042 (mt) REVERT: C 1168 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.6998 (tp) REVERT: C 1191 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7889 (mp10) outliers start: 34 outliers final: 30 residues processed: 146 average time/residue: 0.1482 time to fit residues: 32.4905 Evaluate side-chains 149 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 539 TYR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1112 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1161 THR Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1315 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 ASN C1197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7921 Z= 0.188 Angle : 0.589 9.892 10897 Z= 0.290 Chirality : 0.044 0.275 1336 Planarity : 0.003 0.041 1419 Dihedral : 9.234 160.248 1301 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.29 % Allowed : 21.61 % Favored : 72.10 % 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: -0.61 (0.25), residues: 1180 helix: 0.69 (0.19), residues: 786 sheet: -2.78 (0.62), residues: 68 loop : -2.51 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C1033 HIS 0.003 0.001 HIS C1024 PHE 0.040 0.001 PHE C 314 TYR 0.027 0.002 TYR C 263 ARG 0.003 0.000 ARG C 265 *********************** 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 150 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 0.846 Fit side-chains REVERT: C 253 LEU cc_start: 0.8068 (tp) cc_final: 0.7588 (tp) REVERT: C 412 MET cc_start: 0.6889 (ptp) cc_final: 0.6379 (ptp) REVERT: C 475 TYR cc_start: 0.8438 (t80) cc_final: 0.7835 (t80) REVERT: C 485 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8343 (tt0) REVERT: C 598 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7488 (mtp85) REVERT: C 1027 LEU cc_start: 0.7118 (mt) cc_final: 0.6918 (mt) REVERT: C 1068 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7050 (t80) REVERT: C 1168 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7013 (tp) REVERT: C 1191 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7858 (mt0) outliers start: 32 outliers final: 27 residues processed: 142 average time/residue: 0.1448 time to fit residues: 30.7661 Evaluate side-chains 145 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 539 TYR Chi-restraints excluded: chain C residue 581 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1068 PHE Chi-restraints excluded: chain C residue 1112 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1161 THR Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 103 optimal weight: 40.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN C1197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7921 Z= 0.157 Angle : 0.565 9.828 10897 Z= 0.276 Chirality : 0.043 0.266 1336 Planarity : 0.003 0.044 1419 Dihedral : 9.077 161.563 1301 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.70 % Allowed : 22.20 % Favored : 72.10 % 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: -0.18 (0.25), residues: 1180 helix: 1.07 (0.19), residues: 780 sheet: -2.65 (0.63), residues: 68 loop : -2.42 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1033 HIS 0.002 0.001 HIS C1024 PHE 0.031 0.001 PHE C 314 TYR 0.017 0.001 TYR C 263 ARG 0.003 0.000 ARG C 265 *********************** 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 154 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 0.882 Fit side-chains REVERT: C 412 MET cc_start: 0.6750 (ptp) cc_final: 0.6296 (ptp) REVERT: C 475 TYR cc_start: 0.8358 (t80) cc_final: 0.7750 (t80) REVERT: C 485 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8380 (tt0) REVERT: C 598 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7514 (mtp85) REVERT: C 1037 TRP cc_start: 0.4939 (OUTLIER) cc_final: 0.3821 (t60) REVERT: C 1068 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6995 (t80) REVERT: C 1191 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7817 (mt0) outliers start: 29 outliers final: 23 residues processed: 147 average time/residue: 0.1454 time to fit residues: 31.9517 Evaluate side-chains 145 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 539 TYR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1037 TRP Chi-restraints excluded: chain C residue 1068 PHE Chi-restraints excluded: chain C residue 1112 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 40.0000 chunk 69 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN C1234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7921 Z= 0.279 Angle : 0.656 10.884 10897 Z= 0.326 Chirality : 0.046 0.276 1336 Planarity : 0.004 0.045 1419 Dihedral : 9.349 161.049 1301 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 6.48 % Allowed : 21.81 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1180 helix: 0.73 (0.19), residues: 783 sheet: -2.93 (0.61), residues: 67 loop : -2.45 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 231 HIS 0.004 0.001 HIS C1364 PHE 0.049 0.002 PHE C 314 TYR 0.023 0.002 TYR C 263 ARG 0.004 0.001 ARG C 265 *********************** 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 150 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 0.935 Fit side-chains REVERT: C 253 LEU cc_start: 0.8068 (tp) cc_final: 0.7706 (tp) REVERT: C 412 MET cc_start: 0.6567 (ptp) cc_final: 0.6146 (ptp) REVERT: C 424 ASP cc_start: 0.8099 (t70) cc_final: 0.7590 (t70) REVERT: C 475 TYR cc_start: 0.8508 (t80) cc_final: 0.7940 (t80) REVERT: C 485 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 598 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7496 (mtp85) REVERT: C 1068 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7045 (t80) REVERT: C 1191 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7869 (mt0) outliers start: 33 outliers final: 28 residues processed: 142 average time/residue: 0.1404 time to fit residues: 29.9186 Evaluate side-chains 145 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 539 TYR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1037 TRP Chi-restraints excluded: chain C residue 1068 PHE Chi-restraints excluded: chain C residue 1112 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1161 THR Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1294 TYR Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7921 Z= 0.268 Angle : 0.650 10.093 10897 Z= 0.323 Chirality : 0.046 0.280 1336 Planarity : 0.004 0.045 1419 Dihedral : 9.400 161.219 1301 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.89 % Allowed : 22.99 % Favored : 71.12 % 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: -0.65 (0.25), residues: 1180 helix: 0.66 (0.19), residues: 782 sheet: -2.90 (0.62), residues: 67 loop : -2.50 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C1297 HIS 0.004 0.001 HIS C1364 PHE 0.048 0.002 PHE C 314 TYR 0.039 0.002 TYR C 263 ARG 0.004 0.000 ARG C 265 ********************** 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 151 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: C 253 LEU cc_start: 0.8089 (tp) cc_final: 0.7745 (tp) REVERT: C 370 ARG cc_start: 0.8268 (mpt-90) cc_final: 0.7980 (mpt-90) REVERT: C 412 MET cc_start: 0.6545 (ptp) cc_final: 0.6063 (ptp) REVERT: C 424 ASP cc_start: 0.8064 (t70) cc_final: 0.7668 (t70) REVERT: C 475 TYR cc_start: 0.8494 (t80) cc_final: 0.7839 (t80) REVERT: C 485 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8382 (tm-30) REVERT: C 598 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7752 (mtp85) REVERT: C 1068 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.7065 (t80) REVERT: C 1191 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7865 (mt0) outliers start: 30 outliers final: 28 residues processed: 143 average time/residue: 0.1450 time to fit residues: 30.6564 Evaluate side-chains 150 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 539 TYR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1037 TRP Chi-restraints excluded: chain C residue 1068 PHE Chi-restraints excluded: chain C residue 1112 PHE Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1138 SER Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1161 THR Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1191 GLN Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1294 TYR Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1352 VAL 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: 2.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 93 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.161898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.142809 restraints weight = 14264.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.146091 restraints weight = 6669.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.148216 restraints weight = 3837.393| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7921 Z= 0.156 Angle : 0.586 9.948 10897 Z= 0.286 Chirality : 0.043 0.270 1336 Planarity : 0.003 0.047 1419 Dihedral : 9.097 163.105 1301 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.54 % Allowed : 25.74 % Favored : 70.73 % 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: -0.08 (0.25), residues: 1180 helix: 1.15 (0.19), residues: 780 sheet: -2.60 (0.63), residues: 68 loop : -2.42 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1297 HIS 0.008 0.001 HIS C 867 PHE 0.044 0.001 PHE C 314 TYR 0.029 0.002 TYR C 263 ARG 0.003 0.000 ARG C 265 =============================================================================== Job complete usr+sys time: 1489.96 seconds wall clock time: 27 minutes 42.58 seconds (1662.58 seconds total)