Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 02:34:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/07_2023/5ywd_6853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/07_2023/5ywd_6853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/07_2023/5ywd_6853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/07_2023/5ywd_6853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/07_2023/5ywd_6853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/07_2023/5ywd_6853_updated.pdb" } resolution = 4.2 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 5806 2.51 5 N 1533 2.21 5 O 1605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B ARG 620": "NH1" <-> "NH2" Residue "B ARG 702": "NH1" <-> "NH2" Residue "B ARG 705": "NH1" <-> "NH2" Residue "B ARG 826": "NH1" <-> "NH2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 882": "NH1" <-> "NH2" Residue "B ARG 919": "NH1" <-> "NH2" Residue "B ARG 1099": "NH1" <-> "NH2" Residue "B ARG 1111": "NH1" <-> "NH2" Residue "B ARG 1145": "NH1" <-> "NH2" Residue "B ARG 1183": "NH1" <-> "NH2" Residue "B ARG 1218": "NH1" <-> "NH2" Residue "B ARG 1274": "NH1" <-> "NH2" Residue "B ARG 1300": "NH1" <-> "NH2" Residue "B ARG 1353": "NH1" <-> "NH2" Residue "B ARG 1394": "NH1" <-> "NH2" Residue "B ARG 1402": "NH1" <-> "NH2" Residue "B ARG 1421": "NH1" <-> "NH2" Residue "B ARG 1487": "NH1" <-> "NH2" Residue "B ARG 1498": "NH1" <-> "NH2" Residue "B ARG 1531": "NH1" <-> "NH2" Residue "B ARG 1539": "NH1" <-> "NH2" Residue "B ARG 1554": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 8997 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 8997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 8997 Unusual residues: {' MG': 2, 'ADP': 2} Classifications: {'peptide': 1154, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 36, 'TRANS': 1117, None: 4} Not linked: pdbres="ARG B1579 " pdbres="ADP B2501 " Not linked: pdbres="ADP B2501 " pdbres="ADP B2502 " Not linked: pdbres="ADP B2502 " pdbres=" MG B2503 " Not linked: pdbres=" MG B2503 " pdbres=" MG B2504 " Chain breaks: 7 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 78 Time building chain proxies: 4.55, per 1000 atoms: 0.51 Number of scatterers: 8997 At special positions: 0 Unit cell: (93.895, 78.07, 138.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 4 15.00 Mg 2 11.99 O 1605 8.00 N 1533 7.00 C 5806 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: 3.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 4 sheets defined 63.1% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'B' and resid 224 through 229 removed outlier: 4.492A pdb=" N GLY B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 229' Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.732A pdb=" N ALA B 235 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B 241 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 259 through 275 Processing helix chain 'B' and resid 284 through 295 removed outlier: 3.600A pdb=" N TRP B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 328 Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 356 through 401 removed outlier: 3.763A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 414 through 503 Proline residue: B 436 - end of helix removed outlier: 3.829A pdb=" N ALA B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Proline residue: B 442 - end of helix removed outlier: 4.388A pdb=" N TYR B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL B 458 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N SER B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.800A pdb=" N ALA B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.901A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 563 Proline residue: B 551 - end of helix Processing helix chain 'B' and resid 573 through 614 Proline residue: B 589 - end of helix removed outlier: 3.820A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG B 598 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 599 " --> pdb=" O SER B 595 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 602 " --> pdb=" O ARG B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 796 through 805 removed outlier: 3.686A pdb=" N LYS B 800 " --> pdb=" O LYS B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 832 through 845 removed outlier: 3.688A pdb=" N GLN B 836 " --> pdb=" O GLY B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 894 through 896 No H-bonds generated for 'chain 'B' and resid 894 through 896' Processing helix chain 'B' and resid 914 through 919 Processing helix chain 'B' and resid 1001 through 1008 Processing helix chain 'B' and resid 1012 through 1038 Processing helix chain 'B' and resid 1061 through 1106 removed outlier: 3.576A pdb=" N SER B1073 " --> pdb=" O THR B1069 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B1076 " --> pdb=" O CYS B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1118 through 1134 Processing helix chain 'B' and resid 1136 through 1160 Processing helix chain 'B' and resid 1164 through 1166 No H-bonds generated for 'chain 'B' and resid 1164 through 1166' Processing helix chain 'B' and resid 1168 through 1209 removed outlier: 3.817A pdb=" N VAL B1184 " --> pdb=" O LYS B1180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) Proline residue: B1199 - end of helix Processing helix chain 'B' and resid 1211 through 1217 Processing helix chain 'B' and resid 1220 through 1273 removed outlier: 4.209A pdb=" N LEU B1272 " --> pdb=" O ILE B1268 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1319 removed outlier: 3.825A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B1293 " --> pdb=" O LEU B1289 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN B1296 " --> pdb=" O SER B1292 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1393 Processing helix chain 'B' and resid 1415 through 1419 Processing helix chain 'B' and resid 1436 through 1440 Processing helix chain 'B' and resid 1448 through 1457 Processing helix chain 'B' and resid 1461 through 1465 Processing helix chain 'B' and resid 1484 through 1498 Processing helix chain 'B' and resid 1514 through 1527 removed outlier: 4.040A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1544 Processing sheet with id= A, first strand: chain 'B' and resid 701 through 703 Processing sheet with id= B, first strand: chain 'B' and resid 911 through 913 removed outlier: 3.663A pdb=" N GLY B 912 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 884 " --> pdb=" O THR B 709 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE B 711 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU B 886 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N GLY B 713 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 773 " --> pdb=" O ASP B 854 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 1367 through 1369 Processing sheet with id= D, first strand: chain 'B' and resid 1557 through 1560 removed outlier: 3.951A pdb=" N LEU B1548 " --> pdb=" O LYS B1374 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL B1533 " --> pdb=" O ILE B1375 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE B1377 " --> pdb=" O VAL B1533 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR B1535 " --> pdb=" O ILE B1377 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1635 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: 2.91 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2847 1.34 - 1.46: 2105 1.46 - 1.59: 4133 1.59 - 1.71: 6 1.71 - 1.83: 75 Bond restraints: 9166 Sorted by residual: bond pdb=" C ILE B1136 " pdb=" N PRO B1137 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.36e+00 bond pdb=" C ARG B 297 " pdb=" O ARG B 297 " ideal model delta sigma weight residual 1.237 1.219 0.018 1.17e-02 7.31e+03 2.25e+00 bond pdb=" CB GLN B 369 " pdb=" CG GLN B 369 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CB PHE B 432 " pdb=" CG PHE B 432 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.15e+00 bond pdb=" CB ASN B1293 " pdb=" CG ASN B1293 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.12e+00 ... (remaining 9161 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.49: 285 107.49 - 114.66: 5622 114.66 - 121.84: 4787 121.84 - 129.01: 1681 129.01 - 136.18: 72 Bond angle restraints: 12447 Sorted by residual: angle pdb=" N GLY B 296 " pdb=" CA GLY B 296 " pdb=" C GLY B 296 " ideal model delta sigma weight residual 110.77 122.89 -12.12 1.93e+00 2.68e-01 3.94e+01 angle pdb=" N ALA B 294 " pdb=" CA ALA B 294 " pdb=" C ALA B 294 " ideal model delta sigma weight residual 111.07 116.41 -5.34 1.07e+00 8.73e-01 2.49e+01 angle pdb=" O1B ADP B2501 " pdb=" PB ADP B2501 " pdb=" O3B ADP B2501 " ideal model delta sigma weight residual 119.90 109.75 10.15 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N SER B 302 " pdb=" CA SER B 302 " pdb=" C SER B 302 " ideal model delta sigma weight residual 111.28 107.64 3.64 1.09e+00 8.42e-01 1.11e+01 angle pdb=" O2B ADP B2502 " pdb=" PB ADP B2502 " pdb=" O3B ADP B2502 " ideal model delta sigma weight residual 119.90 109.96 9.94 3.00e+00 1.11e-01 1.10e+01 ... (remaining 12442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 5278 28.72 - 57.43: 179 57.43 - 86.15: 15 86.15 - 114.86: 2 114.86 - 143.58: 2 Dihedral angle restraints: 5476 sinusoidal: 2121 harmonic: 3355 Sorted by residual: dihedral pdb=" C5' ADP B2502 " pdb=" O5' ADP B2502 " pdb=" PA ADP B2502 " pdb=" O2A ADP B2502 " ideal model delta sinusoidal sigma weight residual -60.00 83.58 -143.58 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" O1B ADP B2502 " pdb=" O3A ADP B2502 " pdb=" PB ADP B2502 " pdb=" PA ADP B2502 " ideal model delta sinusoidal sigma weight residual -60.00 -177.39 117.39 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" CA PHE B 566 " pdb=" C PHE B 566 " pdb=" N LYS B 567 " pdb=" CA LYS B 567 " ideal model delta harmonic sigma weight residual -180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 5473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1041 0.036 - 0.073: 332 0.073 - 0.109: 100 0.109 - 0.146: 27 0.146 - 0.182: 2 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA ALA B 294 " pdb=" N ALA B 294 " pdb=" C ALA B 294 " pdb=" CB ALA B 294 " both_signs ideal model delta sigma weight residual False 2.48 2.30 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA TYR B1294 " pdb=" N TYR B1294 " pdb=" C TYR B1294 " pdb=" CB TYR B1294 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE B1504 " pdb=" N ILE B1504 " pdb=" C ILE B1504 " pdb=" CB ILE B1504 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1499 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 550 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO B 551 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 551 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 551 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 432 " 0.016 2.00e-02 2.50e+03 1.23e-02 2.64e+00 pdb=" CG PHE B 432 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE B 432 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 432 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 432 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 432 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 432 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 316 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.97e+00 pdb=" N PRO B 317 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " 0.020 5.00e-02 4.00e+02 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 67 2.60 - 3.18: 7951 3.18 - 3.75: 14266 3.75 - 4.33: 18252 4.33 - 4.90: 30008 Nonbonded interactions: 70544 Sorted by model distance: nonbonded pdb=" OE1 GLN B 775 " pdb="MG MG B2503 " model vdw 2.031 2.170 nonbonded pdb=" O3B ADP B2501 " pdb="MG MG B2503 " model vdw 2.091 2.170 nonbonded pdb=" NE2 GLN B 775 " pdb="MG MG B2503 " model vdw 2.132 2.250 nonbonded pdb=" O PRO B 769 " pdb=" OG1 THR B 848 " model vdw 2.259 2.440 nonbonded pdb=" NE2 HIS B 562 " pdb=" O SER B 569 " model vdw 2.260 2.520 ... (remaining 70539 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=1.00 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: 1.800 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: 0.000 Extract box with map and model: 6.860 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.030 Find NCS groups from input model: 0.240 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 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 : 0.003 0.044 9166 Z= 0.224 Angle : 0.728 12.121 12447 Z= 0.374 Chirality : 0.040 0.182 1502 Planarity : 0.004 0.048 1531 Dihedral : 14.120 143.579 3292 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 6.20 % 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: -1.54 (0.22), residues: 1138 helix: -0.15 (0.17), residues: 737 sheet: -0.89 (0.57), residues: 86 loop : -3.02 (0.28), residues: 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 354 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 20 residues processed: 389 average time/residue: 0.2151 time to fit residues: 114.4214 Evaluate side-chains 227 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0918 time to fit residues: 4.8553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9166 Z= 0.211 Angle : 0.690 9.971 12447 Z= 0.334 Chirality : 0.042 0.209 1502 Planarity : 0.004 0.049 1531 Dihedral : 7.202 133.798 1251 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.52 % 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: -0.07 (0.24), residues: 1138 helix: 0.97 (0.18), residues: 735 sheet: -0.18 (0.54), residues: 86 loop : -2.45 (0.31), residues: 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 257 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 258 average time/residue: 0.1894 time to fit residues: 71.0366 Evaluate side-chains 182 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 ASN ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9166 Z= 0.220 Angle : 0.665 10.255 12447 Z= 0.320 Chirality : 0.041 0.185 1502 Planarity : 0.004 0.048 1531 Dihedral : 6.888 138.167 1251 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1138 helix: 1.55 (0.19), residues: 732 sheet: 0.03 (0.54), residues: 86 loop : -2.07 (0.32), residues: 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 239 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 240 average time/residue: 0.1899 time to fit residues: 66.3637 Evaluate side-chains 177 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9166 Z= 0.194 Angle : 0.662 10.645 12447 Z= 0.314 Chirality : 0.042 0.215 1502 Planarity : 0.004 0.048 1531 Dihedral : 6.586 137.372 1251 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.31 % 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: 0.97 (0.25), residues: 1138 helix: 1.76 (0.19), residues: 729 sheet: 0.20 (0.55), residues: 86 loop : -1.91 (0.33), residues: 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 238 average time/residue: 0.1698 time to fit residues: 60.2793 Evaluate side-chains 180 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.0470 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1538 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9166 Z= 0.180 Angle : 0.662 10.908 12447 Z= 0.310 Chirality : 0.041 0.164 1502 Planarity : 0.003 0.048 1531 Dihedral : 6.478 139.312 1251 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1138 helix: 1.86 (0.19), residues: 741 sheet: 0.28 (0.57), residues: 78 loop : -1.78 (0.33), residues: 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 230 average time/residue: 0.1728 time to fit residues: 59.1544 Evaluate side-chains 173 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 58 optimal weight: 0.0770 chunk 107 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9166 Z= 0.178 Angle : 0.657 11.237 12447 Z= 0.308 Chirality : 0.042 0.195 1502 Planarity : 0.003 0.048 1531 Dihedral : 6.393 137.626 1251 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1138 helix: 1.94 (0.19), residues: 740 sheet: 0.48 (0.59), residues: 78 loop : -1.77 (0.33), residues: 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1811 time to fit residues: 58.2194 Evaluate side-chains 159 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN B1234 ASN ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9166 Z= 0.189 Angle : 0.669 11.527 12447 Z= 0.313 Chirality : 0.042 0.175 1502 Planarity : 0.003 0.048 1531 Dihedral : 6.415 138.009 1251 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1138 helix: 1.89 (0.19), residues: 743 sheet: 0.33 (0.59), residues: 78 loop : -1.73 (0.33), residues: 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1732 time to fit residues: 55.2695 Evaluate side-chains 157 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1521 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9166 Z= 0.190 Angle : 0.695 11.269 12447 Z= 0.327 Chirality : 0.043 0.215 1502 Planarity : 0.003 0.052 1531 Dihedral : 6.409 138.583 1251 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.00 % 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 (0.25), residues: 1138 helix: 1.72 (0.19), residues: 746 sheet: 0.53 (0.60), residues: 78 loop : -1.66 (0.33), residues: 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1691 time to fit residues: 54.9510 Evaluate side-chains 159 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 44 optimal weight: 0.0870 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.0000 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 overall best weight: 0.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1521 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9166 Z= 0.179 Angle : 0.728 11.612 12447 Z= 0.342 Chirality : 0.044 0.224 1502 Planarity : 0.003 0.050 1531 Dihedral : 6.480 135.744 1251 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.00 % 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: 1.08 (0.25), residues: 1138 helix: 1.69 (0.19), residues: 747 sheet: 0.38 (0.60), residues: 78 loop : -1.63 (0.33), residues: 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1705 time to fit residues: 54.3455 Evaluate side-chains 161 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9166 Z= 0.202 Angle : 0.737 11.458 12447 Z= 0.348 Chirality : 0.044 0.207 1502 Planarity : 0.003 0.053 1531 Dihedral : 6.417 133.540 1251 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.00 % 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: 1.14 (0.25), residues: 1138 helix: 1.72 (0.19), residues: 747 sheet: 0.42 (0.61), residues: 78 loop : -1.55 (0.34), residues: 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1723 time to fit residues: 52.6188 Evaluate side-chains 153 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1521 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.096728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078521 restraints weight = 28546.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.080997 restraints weight = 18413.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082746 restraints weight = 13086.683| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9166 Z= 0.173 Angle : 0.710 11.707 12447 Z= 0.336 Chirality : 0.044 0.210 1502 Planarity : 0.003 0.050 1531 Dihedral : 6.277 128.847 1251 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 0.00 % 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: 1.14 (0.25), residues: 1138 helix: 1.69 (0.19), residues: 750 sheet: 0.64 (0.60), residues: 76 loop : -1.57 (0.34), residues: 312 =============================================================================== Job complete usr+sys time: 2049.79 seconds wall clock time: 38 minutes 0.08 seconds (2280.08 seconds total)