Starting phenix.real_space_refine on Sat Apr 6 21:58:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/04_2024/5ywd_6853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/04_2024/5ywd_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_6853/04_2024/5ywd_6853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/04_2024/5ywd_6853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/04_2024/5ywd_6853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywd_6853/04_2024/5ywd_6853_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-dev-5288/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: 5.43, per 1000 atoms: 0.60 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: 3.70 Conformation dependent library (CDL) restraints added in 1.8 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: 2.57 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: 3.15 Time building geometry restraints manager: 3.98 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: 2.020 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: 7.240 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 28.550 Find NCS groups from input model: 0.270 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.000 ------------------------------------------------------------------------------- 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 % Allowed : 8.57 % Favored : 85.23 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1339 HIS 0.009 0.001 HIS B1024 PHE 0.027 0.002 PHE B 432 TYR 0.014 0.002 TYR B 512 ARG 0.009 0.001 ARG B 370 *********************** 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 : 1.105 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: B 226 SER cc_start: 0.9578 (t) cc_final: 0.9352 (p) REVERT: B 243 LYS cc_start: 0.8947 (tttt) cc_final: 0.8609 (mptt) REVERT: B 257 MET cc_start: 0.9155 (mmm) cc_final: 0.8705 (mmm) REVERT: B 314 PHE cc_start: 0.5124 (m-10) cc_final: 0.3953 (m-80) REVERT: B 370 ARG cc_start: 0.9219 (mmt-90) cc_final: 0.8622 (mmp80) REVERT: B 376 SER cc_start: 0.9497 (t) cc_final: 0.9173 (p) REVERT: B 429 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: B 497 LYS cc_start: 0.7549 (mtmt) cc_final: 0.7329 (mtmt) REVERT: B 512 TYR cc_start: 0.8729 (p90) cc_final: 0.8376 (p90) REVERT: B 514 TRP cc_start: 0.8379 (m-10) cc_final: 0.7373 (m-10) REVERT: B 523 GLU cc_start: 0.9064 (tp30) cc_final: 0.8790 (tm-30) REVERT: B 529 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8512 (tm-30) REVERT: B 530 MET cc_start: 0.9529 (tpp) cc_final: 0.9146 (tpp) REVERT: B 547 ASN cc_start: 0.8279 (m-40) cc_final: 0.8011 (m110) REVERT: B 574 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.6675 (p) REVERT: B 580 LEU cc_start: 0.8488 (tp) cc_final: 0.8165 (mt) REVERT: B 581 SER cc_start: 0.9631 (m) cc_final: 0.9411 (p) REVERT: B 685 PHE cc_start: 0.6642 (t80) cc_final: 0.5729 (t80) REVERT: B 696 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.5257 (tp) REVERT: B 778 TRP cc_start: 0.8903 (p-90) cc_final: 0.8542 (p-90) REVERT: B 781 ASN cc_start: 0.8222 (t0) cc_final: 0.7890 (m-40) REVERT: B 855 ASP cc_start: 0.8781 (t0) cc_final: 0.8325 (t0) REVERT: B 861 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.7798 (p0) REVERT: B 868 LEU cc_start: 0.9775 (tp) cc_final: 0.9468 (mm) REVERT: B 891 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 892 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: B 915 LYS cc_start: 0.9438 (mttt) cc_final: 0.9106 (tppt) REVERT: B 1011 LEU cc_start: 0.8630 (tp) cc_final: 0.8407 (pt) REVERT: B 1012 LEU cc_start: 0.9076 (mt) cc_final: 0.8771 (mp) REVERT: B 1079 CYS cc_start: 0.9220 (t) cc_final: 0.8804 (p) REVERT: B 1087 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8670 (mm-30) REVERT: B 1092 LYS cc_start: 0.9187 (mttm) cc_final: 0.8643 (tptt) REVERT: B 1096 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8190 (tmt170) REVERT: B 1114 GLU cc_start: 0.8751 (tt0) cc_final: 0.8402 (tm-30) REVERT: B 1194 ASP cc_start: 0.9293 (t0) cc_final: 0.9086 (m-30) REVERT: B 1202 SER cc_start: 0.9244 (m) cc_final: 0.8162 (p) REVERT: B 1220 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9185 (mp0) REVERT: B 1222 ARG cc_start: 0.9217 (mmt-90) cc_final: 0.8453 (mmm160) REVERT: B 1246 ARG cc_start: 0.8823 (mmt-90) cc_final: 0.8094 (mmm-85) REVERT: B 1281 VAL cc_start: 0.9708 (t) cc_final: 0.9457 (p) REVERT: B 1395 MET cc_start: 0.8874 (mmt) cc_final: 0.8494 (mmm) REVERT: B 1425 ILE cc_start: 0.9213 (mt) cc_final: 0.8652 (mt) REVERT: B 1505 MET cc_start: 0.8052 (ttm) cc_final: 0.7675 (mmt) REVERT: B 1507 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8310 (mp0) REVERT: B 1517 GLU cc_start: 0.9090 (tp30) cc_final: 0.8852 (tp30) REVERT: B 1536 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8269 (mp) REVERT: B 1552 LEU cc_start: 0.9618 (mt) cc_final: 0.9220 (tp) outliers start: 60 outliers final: 20 residues processed: 389 average time/residue: 0.2142 time to fit residues: 113.4014 Evaluate side-chains 250 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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: 3.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 B1245 ASN B1348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9166 Z= 0.231 Angle : 0.689 9.905 12447 Z= 0.336 Chirality : 0.043 0.208 1502 Planarity : 0.004 0.045 1531 Dihedral : 7.269 135.241 1251 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.41 % Allowed : 4.03 % Favored : 95.56 % 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: -0.01 (0.24), residues: 1138 helix: 1.05 (0.18), residues: 732 sheet: -0.24 (0.55), residues: 86 loop : -2.45 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 778 HIS 0.008 0.001 HIS B 562 PHE 0.045 0.002 PHE B1240 TYR 0.016 0.001 TYR B 454 ARG 0.005 0.001 ARG B1353 *********************** 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 270 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 266 time to evaluate : 0.988 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: B 218 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8903 (pp) REVERT: B 233 MET cc_start: 0.9423 (tpp) cc_final: 0.9075 (tpp) REVERT: B 243 LYS cc_start: 0.8993 (tttt) cc_final: 0.8596 (mptt) REVERT: B 291 LEU cc_start: 0.9058 (mt) cc_final: 0.8709 (mt) REVERT: B 314 PHE cc_start: 0.5214 (m-10) cc_final: 0.4969 (m-80) REVERT: B 419 ASN cc_start: 0.8989 (m-40) cc_final: 0.8704 (m110) REVERT: B 421 VAL cc_start: 0.8302 (t) cc_final: 0.8049 (t) REVERT: B 512 TYR cc_start: 0.8679 (p90) cc_final: 0.7426 (p90) REVERT: B 514 TRP cc_start: 0.8546 (m-10) cc_final: 0.7334 (m-10) REVERT: B 529 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8586 (tm-30) REVERT: B 719 LYS cc_start: 0.9553 (mtmt) cc_final: 0.9018 (mttm) REVERT: B 778 TRP cc_start: 0.9217 (p-90) cc_final: 0.8633 (p-90) REVERT: B 781 ASN cc_start: 0.8155 (t0) cc_final: 0.7571 (m-40) REVERT: B 846 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8179 (mm-40) REVERT: B 855 ASP cc_start: 0.8945 (t0) cc_final: 0.8362 (t0) REVERT: B 869 MET cc_start: 0.9153 (tpp) cc_final: 0.8504 (tpp) REVERT: B 893 TYR cc_start: 0.8534 (m-10) cc_final: 0.8133 (m-80) REVERT: B 903 MET cc_start: 0.8199 (mmp) cc_final: 0.7919 (mmm) REVERT: B 915 LYS cc_start: 0.9553 (mttt) cc_final: 0.9237 (tptt) REVERT: B 1005 LEU cc_start: 0.8592 (mt) cc_final: 0.8353 (pp) REVERT: B 1011 LEU cc_start: 0.8688 (tp) cc_final: 0.8433 (pt) REVERT: B 1012 LEU cc_start: 0.9064 (mt) cc_final: 0.8812 (mp) REVERT: B 1064 TYR cc_start: 0.9031 (m-80) cc_final: 0.8782 (m-80) REVERT: B 1079 CYS cc_start: 0.9241 (t) cc_final: 0.8915 (p) REVERT: B 1092 LYS cc_start: 0.9245 (mttm) cc_final: 0.8695 (tptt) REVERT: B 1096 ARG cc_start: 0.8769 (tpp80) cc_final: 0.8341 (ttm170) REVERT: B 1114 GLU cc_start: 0.8818 (tt0) cc_final: 0.8493 (tm-30) REVERT: B 1202 SER cc_start: 0.9183 (m) cc_final: 0.8130 (p) REVERT: B 1206 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8389 (mt-10) REVERT: B 1222 ARG cc_start: 0.9063 (mmt-90) cc_final: 0.8268 (mmm160) REVERT: B 1425 ILE cc_start: 0.8858 (mt) cc_final: 0.8052 (mt) REVERT: B 1488 GLN cc_start: 0.9684 (tp40) cc_final: 0.9207 (mt0) REVERT: B 1505 MET cc_start: 0.7909 (ttm) cc_final: 0.7561 (mmt) REVERT: B 1507 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8403 (mp0) REVERT: B 1517 GLU cc_start: 0.9095 (tp30) cc_final: 0.8708 (tp30) REVERT: B 1552 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9123 (tp) outliers start: 4 outliers final: 0 residues processed: 267 average time/residue: 0.1931 time to fit residues: 73.3872 Evaluate side-chains 201 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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: 0.3980 chunk 32 optimal weight: 0.0770 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9166 Z= 0.177 Angle : 0.643 10.268 12447 Z= 0.306 Chirality : 0.041 0.175 1502 Planarity : 0.004 0.082 1531 Dihedral : 6.768 138.126 1251 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.31 % Allowed : 3.72 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1138 helix: 1.59 (0.19), residues: 732 sheet: 0.11 (0.54), residues: 86 loop : -2.02 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 231 HIS 0.006 0.001 HIS B1024 PHE 0.020 0.002 PHE B 433 TYR 0.015 0.001 TYR B 454 ARG 0.009 0.000 ARG B 388 *********************** 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 270 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 267 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8885 (pp) REVERT: B 243 LYS cc_start: 0.8935 (tttt) cc_final: 0.8550 (mptt) REVERT: B 295 PHE cc_start: 0.7321 (m-10) cc_final: 0.6069 (m-10) REVERT: B 314 PHE cc_start: 0.5415 (m-10) cc_final: 0.5087 (m-80) REVERT: B 387 LEU cc_start: 0.9600 (tp) cc_final: 0.9377 (tp) REVERT: B 419 ASN cc_start: 0.9016 (m-40) cc_final: 0.8681 (m110) REVERT: B 502 MET cc_start: 0.9524 (ttt) cc_final: 0.8559 (tmm) REVERT: B 512 TYR cc_start: 0.8584 (p90) cc_final: 0.7443 (p90) REVERT: B 514 TRP cc_start: 0.8474 (m-10) cc_final: 0.7389 (m-10) REVERT: B 529 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8676 (tm-30) REVERT: B 685 PHE cc_start: 0.7337 (t80) cc_final: 0.7126 (t80) REVERT: B 719 LYS cc_start: 0.9573 (mtmt) cc_final: 0.8999 (mttm) REVERT: B 730 MET cc_start: 0.6445 (ttp) cc_final: 0.6237 (ttt) REVERT: B 778 TRP cc_start: 0.9128 (p-90) cc_final: 0.8639 (p-90) REVERT: B 781 ASN cc_start: 0.8217 (t0) cc_final: 0.7653 (m-40) REVERT: B 846 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8131 (mm-40) REVERT: B 855 ASP cc_start: 0.8948 (t0) cc_final: 0.8366 (t0) REVERT: B 876 LEU cc_start: 0.9197 (tp) cc_final: 0.8900 (tp) REVERT: B 903 MET cc_start: 0.8152 (mmp) cc_final: 0.7777 (mmm) REVERT: B 915 LYS cc_start: 0.9549 (mttt) cc_final: 0.9226 (tptt) REVERT: B 1005 LEU cc_start: 0.8595 (mt) cc_final: 0.8374 (pp) REVERT: B 1011 LEU cc_start: 0.8530 (tp) cc_final: 0.8285 (pt) REVERT: B 1012 LEU cc_start: 0.9056 (mt) cc_final: 0.8779 (mp) REVERT: B 1079 CYS cc_start: 0.9233 (t) cc_final: 0.8910 (p) REVERT: B 1092 LYS cc_start: 0.9110 (mttm) cc_final: 0.8668 (tptt) REVERT: B 1096 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8156 (tmt170) REVERT: B 1114 GLU cc_start: 0.8841 (tt0) cc_final: 0.8517 (tm-30) REVERT: B 1202 SER cc_start: 0.9187 (m) cc_final: 0.8101 (p) REVERT: B 1206 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8356 (mt-10) REVERT: B 1222 ARG cc_start: 0.8811 (mmt-90) cc_final: 0.8204 (tpp80) REVERT: B 1246 ARG cc_start: 0.8511 (mmt180) cc_final: 0.8150 (mmt-90) REVERT: B 1305 MET cc_start: 0.8162 (tmm) cc_final: 0.7954 (tmm) REVERT: B 1398 MET cc_start: 0.6599 (ttt) cc_final: 0.6240 (ttp) REVERT: B 1507 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8433 (mp0) REVERT: B 1517 GLU cc_start: 0.9075 (tp30) cc_final: 0.8727 (tp30) REVERT: B 1525 MET cc_start: 0.9328 (tmm) cc_final: 0.9056 (tmm) REVERT: B 1552 LEU cc_start: 0.9581 (mt) cc_final: 0.9172 (tp) outliers start: 3 outliers final: 0 residues processed: 268 average time/residue: 0.1961 time to fit residues: 75.0978 Evaluate side-chains 203 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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: 3.9990 chunk 78 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 ASN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 HIS ** B1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9166 Z= 0.231 Angle : 0.684 10.754 12447 Z= 0.326 Chirality : 0.041 0.182 1502 Planarity : 0.004 0.052 1531 Dihedral : 6.479 133.370 1251 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.21 % Allowed : 4.13 % Favored : 95.66 % 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: 0.98 (0.25), residues: 1138 helix: 1.72 (0.19), residues: 731 sheet: 0.49 (0.57), residues: 86 loop : -1.89 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 899 HIS 0.005 0.001 HIS B1024 PHE 0.021 0.002 PHE B 433 TYR 0.014 0.001 TYR B 454 ARG 0.006 0.000 ARG B 388 *********************** 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 244 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 1.032 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: B 243 LYS cc_start: 0.8930 (tttt) cc_final: 0.8534 (mptt) REVERT: B 314 PHE cc_start: 0.5539 (m-10) cc_final: 0.4694 (m-80) REVERT: B 421 VAL cc_start: 0.8091 (t) cc_final: 0.7839 (t) REVERT: B 502 MET cc_start: 0.9515 (ttt) cc_final: 0.8603 (tmm) REVERT: B 512 TYR cc_start: 0.8584 (p90) cc_final: 0.7437 (p90) REVERT: B 719 LYS cc_start: 0.9622 (mtmt) cc_final: 0.9059 (mttm) REVERT: B 781 ASN cc_start: 0.8356 (t0) cc_final: 0.8091 (m-40) REVERT: B 789 THR cc_start: 0.9164 (p) cc_final: 0.8945 (t) REVERT: B 801 MET cc_start: 0.9262 (tmm) cc_final: 0.8992 (tmm) REVERT: B 846 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8196 (mm-40) REVERT: B 855 ASP cc_start: 0.9039 (t0) cc_final: 0.8588 (t0) REVERT: B 900 ILE cc_start: 0.9459 (mp) cc_final: 0.9248 (pt) REVERT: B 903 MET cc_start: 0.8033 (mmp) cc_final: 0.7518 (mmm) REVERT: B 915 LYS cc_start: 0.9589 (mttt) cc_final: 0.9309 (tptt) REVERT: B 1005 LEU cc_start: 0.8645 (mt) cc_final: 0.8385 (pp) REVERT: B 1011 LEU cc_start: 0.8642 (tp) cc_final: 0.8394 (pt) REVERT: B 1012 LEU cc_start: 0.9126 (mt) cc_final: 0.8888 (mp) REVERT: B 1079 CYS cc_start: 0.9271 (t) cc_final: 0.8927 (p) REVERT: B 1092 LYS cc_start: 0.9144 (mttm) cc_final: 0.8651 (tptt) REVERT: B 1110 MET cc_start: 0.8520 (mmm) cc_final: 0.8296 (mmm) REVERT: B 1114 GLU cc_start: 0.8830 (tt0) cc_final: 0.8493 (tm-30) REVERT: B 1202 SER cc_start: 0.9190 (m) cc_final: 0.8349 (p) REVERT: B 1222 ARG cc_start: 0.8806 (mmt-90) cc_final: 0.8208 (tpp80) REVERT: B 1507 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8680 (tt0) REVERT: B 1517 GLU cc_start: 0.9104 (tp30) cc_final: 0.8819 (tp30) REVERT: B 1525 MET cc_start: 0.9381 (tmm) cc_final: 0.9112 (tmm) REVERT: B 1539 ARG cc_start: 0.9225 (mmp-170) cc_final: 0.8927 (mmp-170) REVERT: B 1552 LEU cc_start: 0.9697 (mt) cc_final: 0.9254 (tp) outliers start: 2 outliers final: 0 residues processed: 243 average time/residue: 0.1804 time to fit residues: 63.0956 Evaluate side-chains 183 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 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 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 889 HIS ** 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: 0.7588 moved from start: 0.5087 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= 0.212 Angle : 0.664 10.970 12447 Z= 0.315 Chirality : 0.041 0.175 1502 Planarity : 0.003 0.053 1531 Dihedral : 6.210 125.157 1251 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.21 % Allowed : 2.17 % Favored : 97.62 % 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: 1.06 (0.25), residues: 1138 helix: 1.78 (0.19), residues: 731 sheet: 0.56 (0.57), residues: 86 loop : -1.86 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 232 HIS 0.005 0.001 HIS B1024 PHE 0.025 0.002 PHE B1204 TYR 0.017 0.001 TYR B 378 ARG 0.003 0.000 ARG B 798 *********************** 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 242 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 1.039 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: B 243 LYS cc_start: 0.8930 (tttt) cc_final: 0.8531 (mptt) REVERT: B 257 MET cc_start: 0.8996 (mtp) cc_final: 0.8739 (mtp) REVERT: B 383 THR cc_start: 0.9676 (m) cc_final: 0.9464 (p) REVERT: B 429 MET cc_start: 0.7955 (mtt) cc_final: 0.7474 (mmt) REVERT: B 433 PHE cc_start: 0.6880 (m-10) cc_final: 0.6586 (m-80) REVERT: B 502 MET cc_start: 0.9513 (ttt) cc_final: 0.8575 (tmm) REVERT: B 512 TYR cc_start: 0.8678 (p90) cc_final: 0.7449 (p90) REVERT: B 719 LYS cc_start: 0.9558 (mtmt) cc_final: 0.9209 (mtpp) REVERT: B 789 THR cc_start: 0.9268 (p) cc_final: 0.9049 (t) REVERT: B 846 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8240 (mm-40) REVERT: B 855 ASP cc_start: 0.9035 (t0) cc_final: 0.8569 (t0) REVERT: B 903 MET cc_start: 0.8050 (mmp) cc_final: 0.7528 (mmm) REVERT: B 915 LYS cc_start: 0.9577 (mttt) cc_final: 0.9303 (tptt) REVERT: B 1005 LEU cc_start: 0.8637 (mt) cc_final: 0.8396 (pp) REVERT: B 1011 LEU cc_start: 0.8320 (tp) cc_final: 0.8113 (pt) REVERT: B 1012 LEU cc_start: 0.9131 (mt) cc_final: 0.8911 (mp) REVERT: B 1079 CYS cc_start: 0.9281 (t) cc_final: 0.8957 (p) REVERT: B 1092 LYS cc_start: 0.9073 (mttm) cc_final: 0.8639 (tptt) REVERT: B 1114 GLU cc_start: 0.8793 (tt0) cc_final: 0.8444 (tm-30) REVERT: B 1202 SER cc_start: 0.9218 (m) cc_final: 0.8889 (p) REVERT: B 1219 TYR cc_start: 0.8876 (m-80) cc_final: 0.8618 (m-10) REVERT: B 1222 ARG cc_start: 0.8791 (mmt-90) cc_final: 0.8263 (ttm170) REVERT: B 1246 ARG cc_start: 0.8658 (mmt-90) cc_final: 0.8314 (mmt-90) REVERT: B 1503 PHE cc_start: 0.8101 (m-10) cc_final: 0.7900 (m-10) REVERT: B 1505 MET cc_start: 0.8128 (mmp) cc_final: 0.7892 (mmp) REVERT: B 1507 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8745 (tt0) REVERT: B 1517 GLU cc_start: 0.9077 (tp30) cc_final: 0.8771 (tp30) REVERT: B 1525 MET cc_start: 0.9374 (tmm) cc_final: 0.9112 (tmm) REVERT: B 1552 LEU cc_start: 0.9724 (mt) cc_final: 0.9274 (tp) outliers start: 2 outliers final: 0 residues processed: 241 average time/residue: 0.1891 time to fit residues: 66.0382 Evaluate side-chains 186 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1234 ASN ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9166 Z= 0.250 Angle : 0.696 10.834 12447 Z= 0.335 Chirality : 0.043 0.185 1502 Planarity : 0.004 0.050 1531 Dihedral : 6.123 115.097 1251 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: 0.96 (0.25), residues: 1138 helix: 1.67 (0.19), residues: 740 sheet: 0.46 (0.57), residues: 86 loop : -1.88 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 232 HIS 0.006 0.001 HIS B1098 PHE 0.022 0.002 PHE B 372 TYR 0.012 0.001 TYR B 378 ARG 0.007 0.000 ARG B 526 *********************** 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 230 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8133 (tm-30) REVERT: B 233 MET cc_start: 0.9299 (mmp) cc_final: 0.9063 (tpp) REVERT: B 383 THR cc_start: 0.9676 (m) cc_final: 0.9395 (p) REVERT: B 433 PHE cc_start: 0.6910 (m-10) cc_final: 0.6617 (m-80) REVERT: B 502 MET cc_start: 0.9491 (ttt) cc_final: 0.8701 (tmm) REVERT: B 512 TYR cc_start: 0.8721 (p90) cc_final: 0.7509 (p90) REVERT: B 719 LYS cc_start: 0.9594 (mtmt) cc_final: 0.9187 (mttm) REVERT: B 801 MET cc_start: 0.9423 (tmm) cc_final: 0.9112 (tmm) REVERT: B 846 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8345 (mm-40) REVERT: B 855 ASP cc_start: 0.9022 (t0) cc_final: 0.8417 (t0) REVERT: B 876 LEU cc_start: 0.9101 (tt) cc_final: 0.8750 (mm) REVERT: B 903 MET cc_start: 0.8104 (mmp) cc_final: 0.7706 (mmm) REVERT: B 915 LYS cc_start: 0.9577 (mttt) cc_final: 0.9311 (tptt) REVERT: B 1005 LEU cc_start: 0.8672 (mt) cc_final: 0.8404 (pp) REVERT: B 1079 CYS cc_start: 0.9299 (t) cc_final: 0.8983 (p) REVERT: B 1092 LYS cc_start: 0.9094 (mttm) cc_final: 0.8665 (tptt) REVERT: B 1114 GLU cc_start: 0.8775 (tt0) cc_final: 0.8452 (tm-30) REVERT: B 1202 SER cc_start: 0.9266 (m) cc_final: 0.8914 (p) REVERT: B 1246 ARG cc_start: 0.8732 (mmt-90) cc_final: 0.8275 (mmt-90) REVERT: B 1507 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8838 (mp0) REVERT: B 1517 GLU cc_start: 0.9126 (tp30) cc_final: 0.8823 (tp30) REVERT: B 1525 MET cc_start: 0.9365 (tmm) cc_final: 0.9079 (tmm) REVERT: B 1536 ILE cc_start: 0.8687 (pt) cc_final: 0.7534 (pt) REVERT: B 1552 LEU cc_start: 0.9693 (mt) cc_final: 0.9242 (tp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1991 time to fit residues: 67.3915 Evaluate side-chains 172 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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: 2.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5752 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= 0.180 Angle : 0.682 11.450 12447 Z= 0.317 Chirality : 0.042 0.163 1502 Planarity : 0.003 0.051 1531 Dihedral : 5.913 110.066 1251 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 1.13 (0.25), residues: 1138 helix: 1.82 (0.19), residues: 741 sheet: 0.41 (0.56), residues: 86 loop : -1.85 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 778 HIS 0.005 0.001 HIS B1098 PHE 0.021 0.001 PHE B 372 TYR 0.022 0.001 TYR B 893 ARG 0.004 0.000 ARG B 521 *********************** 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 230 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.011 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: B 219 GLN cc_start: 0.8301 (tm-30) cc_final: 0.8014 (tm-30) REVERT: B 383 THR cc_start: 0.9652 (m) cc_final: 0.9383 (p) REVERT: B 429 MET cc_start: 0.8052 (mtt) cc_final: 0.7657 (mtt) REVERT: B 502 MET cc_start: 0.9450 (ttt) cc_final: 0.8332 (tmm) REVERT: B 506 MET cc_start: 0.8084 (tpp) cc_final: 0.7835 (tpt) REVERT: B 512 TYR cc_start: 0.8544 (p90) cc_final: 0.7448 (p90) REVERT: B 523 GLU cc_start: 0.9099 (mp0) cc_final: 0.8861 (pp20) REVERT: B 710 MET cc_start: 0.8955 (mmp) cc_final: 0.8578 (mmp) REVERT: B 719 LYS cc_start: 0.9551 (mtmt) cc_final: 0.9137 (mttm) REVERT: B 801 MET cc_start: 0.9395 (tmm) cc_final: 0.8972 (tmm) REVERT: B 846 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8149 (mm110) REVERT: B 855 ASP cc_start: 0.8840 (t0) cc_final: 0.8304 (t0) REVERT: B 869 MET cc_start: 0.9063 (tpp) cc_final: 0.8784 (tpp) REVERT: B 876 LEU cc_start: 0.9099 (tt) cc_final: 0.8746 (mm) REVERT: B 903 MET cc_start: 0.8086 (mmp) cc_final: 0.7737 (mmm) REVERT: B 915 LYS cc_start: 0.9573 (mttt) cc_final: 0.9302 (tptt) REVERT: B 1005 LEU cc_start: 0.8673 (mt) cc_final: 0.8421 (pp) REVERT: B 1079 CYS cc_start: 0.9252 (t) cc_final: 0.8940 (p) REVERT: B 1092 LYS cc_start: 0.9073 (mttm) cc_final: 0.8627 (tptt) REVERT: B 1114 GLU cc_start: 0.8707 (tt0) cc_final: 0.8384 (tm-30) REVERT: B 1202 SER cc_start: 0.9228 (m) cc_final: 0.8877 (p) REVERT: B 1246 ARG cc_start: 0.8678 (mmt-90) cc_final: 0.8459 (mmt-90) REVERT: B 1507 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8906 (mp0) REVERT: B 1525 MET cc_start: 0.9368 (tmm) cc_final: 0.9061 (tmm) REVERT: B 1536 ILE cc_start: 0.8659 (pt) cc_final: 0.7519 (pt) REVERT: B 1552 LEU cc_start: 0.9689 (mt) cc_final: 0.9229 (tp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1741 time to fit residues: 59.1646 Evaluate side-chains 180 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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: 0.7980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 889 HIS ** 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: 0.7568 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9166 Z= 0.191 Angle : 0.686 11.449 12447 Z= 0.321 Chirality : 0.042 0.153 1502 Planarity : 0.003 0.050 1531 Dihedral : 5.804 104.404 1251 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 1.78 (0.19), residues: 741 sheet: 0.46 (0.56), residues: 86 loop : -1.79 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 778 HIS 0.005 0.001 HIS B1098 PHE 0.049 0.002 PHE B 433 TYR 0.036 0.001 TYR B 893 ARG 0.005 0.000 ARG B1353 *********************** 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 223 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8135 (tm-30) REVERT: B 233 MET cc_start: 0.9050 (mmp) cc_final: 0.8681 (tpp) REVERT: B 320 ILE cc_start: 0.9337 (mt) cc_final: 0.8398 (mt) REVERT: B 323 ILE cc_start: 0.8154 (pt) cc_final: 0.7814 (pt) REVERT: B 383 THR cc_start: 0.9645 (m) cc_final: 0.9365 (p) REVERT: B 502 MET cc_start: 0.9425 (ttt) cc_final: 0.8371 (tmm) REVERT: B 506 MET cc_start: 0.8050 (tpp) cc_final: 0.7719 (tpt) REVERT: B 512 TYR cc_start: 0.8549 (p90) cc_final: 0.7406 (p90) REVERT: B 719 LYS cc_start: 0.9575 (mtmt) cc_final: 0.9195 (mttm) REVERT: B 801 MET cc_start: 0.9371 (tmm) cc_final: 0.8941 (tmm) REVERT: B 846 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8191 (mm110) REVERT: B 855 ASP cc_start: 0.8872 (t0) cc_final: 0.8334 (t0) REVERT: B 876 LEU cc_start: 0.9156 (tt) cc_final: 0.8802 (mm) REVERT: B 903 MET cc_start: 0.8112 (mmp) cc_final: 0.7784 (mmm) REVERT: B 915 LYS cc_start: 0.9554 (mttt) cc_final: 0.9314 (tptt) REVERT: B 1005 LEU cc_start: 0.8699 (mt) cc_final: 0.8467 (pp) REVERT: B 1079 CYS cc_start: 0.9435 (t) cc_final: 0.9024 (p) REVERT: B 1092 LYS cc_start: 0.9032 (mttm) cc_final: 0.8576 (tptt) REVERT: B 1114 GLU cc_start: 0.8709 (tt0) cc_final: 0.8403 (tm-30) REVERT: B 1202 SER cc_start: 0.9190 (m) cc_final: 0.8822 (p) REVERT: B 1229 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8749 (tm-30) REVERT: B 1285 LEU cc_start: 0.9378 (mm) cc_final: 0.8602 (tt) REVERT: B 1398 MET cc_start: 0.6424 (ttt) cc_final: 0.6195 (ttm) REVERT: B 1503 PHE cc_start: 0.7866 (m-10) cc_final: 0.7507 (m-10) REVERT: B 1505 MET cc_start: 0.8065 (mmp) cc_final: 0.7338 (mtm) REVERT: B 1507 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8604 (mp0) REVERT: B 1525 MET cc_start: 0.9364 (tmm) cc_final: 0.9036 (tmm) REVERT: B 1536 ILE cc_start: 0.8637 (pt) cc_final: 0.7712 (pt) REVERT: B 1552 LEU cc_start: 0.9662 (mt) cc_final: 0.9143 (tp) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1762 time to fit residues: 58.6799 Evaluate side-chains 184 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 547 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: 0.7571 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9166 Z= 0.191 Angle : 0.683 11.795 12447 Z= 0.319 Chirality : 0.042 0.154 1502 Planarity : 0.003 0.052 1531 Dihedral : 5.715 99.729 1251 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1138 helix: 1.78 (0.19), residues: 740 sheet: 0.53 (0.59), residues: 78 loop : -1.78 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 778 HIS 0.005 0.001 HIS B1024 PHE 0.051 0.002 PHE B 433 TYR 0.028 0.001 TYR B 893 ARG 0.005 0.000 ARG B 495 *********************** 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 229 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7896 (tm-30) REVERT: B 233 MET cc_start: 0.9162 (mmp) cc_final: 0.8830 (tpp) REVERT: B 320 ILE cc_start: 0.9267 (mt) cc_final: 0.8361 (mt) REVERT: B 323 ILE cc_start: 0.8160 (pt) cc_final: 0.7860 (pt) REVERT: B 383 THR cc_start: 0.9643 (m) cc_final: 0.9355 (p) REVERT: B 502 MET cc_start: 0.9451 (ttt) cc_final: 0.8409 (tmm) REVERT: B 506 MET cc_start: 0.8162 (tpp) cc_final: 0.7738 (tpt) REVERT: B 512 TYR cc_start: 0.8577 (p90) cc_final: 0.7383 (p90) REVERT: B 717 CYS cc_start: 0.7597 (m) cc_final: 0.7370 (m) REVERT: B 719 LYS cc_start: 0.9578 (mtmt) cc_final: 0.9161 (mttm) REVERT: B 801 MET cc_start: 0.9365 (tmm) cc_final: 0.8927 (tmm) REVERT: B 846 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8240 (mm110) REVERT: B 855 ASP cc_start: 0.8857 (t0) cc_final: 0.8313 (t0) REVERT: B 868 LEU cc_start: 0.9704 (tp) cc_final: 0.9422 (mm) REVERT: B 876 LEU cc_start: 0.9152 (tt) cc_final: 0.8779 (mm) REVERT: B 890 LYS cc_start: 0.8157 (mtpp) cc_final: 0.7896 (mtpp) REVERT: B 893 TYR cc_start: 0.7479 (m-80) cc_final: 0.6832 (m-80) REVERT: B 903 MET cc_start: 0.8157 (mmp) cc_final: 0.7640 (mmm) REVERT: B 915 LYS cc_start: 0.9553 (mttt) cc_final: 0.9318 (tptt) REVERT: B 1005 LEU cc_start: 0.8706 (mt) cc_final: 0.8462 (pp) REVERT: B 1079 CYS cc_start: 0.9395 (t) cc_final: 0.8990 (p) REVERT: B 1092 LYS cc_start: 0.9031 (mttm) cc_final: 0.8577 (tptt) REVERT: B 1114 GLU cc_start: 0.8705 (tt0) cc_final: 0.8419 (tm-30) REVERT: B 1202 SER cc_start: 0.9192 (m) cc_final: 0.8852 (p) REVERT: B 1285 LEU cc_start: 0.9392 (mm) cc_final: 0.8611 (tt) REVERT: B 1398 MET cc_start: 0.6545 (ttt) cc_final: 0.6217 (ttt) REVERT: B 1505 MET cc_start: 0.8244 (mmp) cc_final: 0.7299 (mtm) REVERT: B 1525 MET cc_start: 0.9347 (tmm) cc_final: 0.9007 (tmm) REVERT: B 1539 ARG cc_start: 0.9169 (mmp-170) cc_final: 0.8964 (mmp-170) REVERT: B 1552 LEU cc_start: 0.9656 (mt) cc_final: 0.9132 (tp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1794 time to fit residues: 59.8718 Evaluate side-chains 183 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 91 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 547 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: 0.7550 moved from start: 0.6365 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= 0.169 Angle : 0.705 11.852 12447 Z= 0.329 Chirality : 0.042 0.159 1502 Planarity : 0.003 0.050 1531 Dihedral : 5.608 93.923 1251 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 1.03 (0.25), residues: 1138 helix: 1.71 (0.19), residues: 742 sheet: 0.57 (0.59), residues: 78 loop : -1.83 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 778 HIS 0.006 0.001 HIS B1316 PHE 0.051 0.002 PHE B 433 TYR 0.024 0.001 TYR B 893 ARG 0.003 0.000 ARG B 526 ********************** 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 233 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.057 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: B 219 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 233 MET cc_start: 0.9104 (mmp) cc_final: 0.8824 (tpp) REVERT: B 320 ILE cc_start: 0.9266 (mt) cc_final: 0.8347 (mt) REVERT: B 323 ILE cc_start: 0.8180 (pt) cc_final: 0.7886 (pt) REVERT: B 383 THR cc_start: 0.9627 (m) cc_final: 0.9379 (p) REVERT: B 429 MET cc_start: 0.8258 (mmt) cc_final: 0.7291 (mmp) REVERT: B 502 MET cc_start: 0.9451 (ttt) cc_final: 0.8395 (tmm) REVERT: B 506 MET cc_start: 0.8284 (tpp) cc_final: 0.7772 (tpt) REVERT: B 512 TYR cc_start: 0.8510 (p90) cc_final: 0.7369 (p90) REVERT: B 717 CYS cc_start: 0.7586 (m) cc_final: 0.7267 (m) REVERT: B 719 LYS cc_start: 0.9558 (mtmt) cc_final: 0.9195 (mttp) REVERT: B 801 MET cc_start: 0.9355 (tmm) cc_final: 0.8988 (tmm) REVERT: B 846 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8201 (mm110) REVERT: B 855 ASP cc_start: 0.8819 (t0) cc_final: 0.8276 (t0) REVERT: B 868 LEU cc_start: 0.9692 (tp) cc_final: 0.9430 (mm) REVERT: B 903 MET cc_start: 0.8138 (mmp) cc_final: 0.7806 (mmm) REVERT: B 915 LYS cc_start: 0.9559 (mttt) cc_final: 0.9320 (tptt) REVERT: B 1005 LEU cc_start: 0.8687 (mt) cc_final: 0.8450 (pp) REVERT: B 1079 CYS cc_start: 0.9481 (t) cc_final: 0.9017 (p) REVERT: B 1092 LYS cc_start: 0.9006 (mttm) cc_final: 0.8549 (tptt) REVERT: B 1114 GLU cc_start: 0.8684 (tt0) cc_final: 0.8338 (tm-30) REVERT: B 1202 SER cc_start: 0.9213 (m) cc_final: 0.8879 (p) REVERT: B 1246 ARG cc_start: 0.8624 (mmt-90) cc_final: 0.8414 (mmt-90) REVERT: B 1285 LEU cc_start: 0.9367 (mm) cc_final: 0.8597 (tt) REVERT: B 1505 MET cc_start: 0.8257 (mmp) cc_final: 0.7457 (mtm) REVERT: B 1525 MET cc_start: 0.9330 (tmm) cc_final: 0.8993 (tmm) REVERT: B 1552 LEU cc_start: 0.9670 (mt) cc_final: 0.9175 (tp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1831 time to fit residues: 62.8682 Evaluate side-chains 180 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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: 3.9990 chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076381 restraints weight = 28943.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078784 restraints weight = 18464.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.080568 restraints weight = 13067.914| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9166 Z= 0.183 Angle : 0.704 11.798 12447 Z= 0.328 Chirality : 0.043 0.217 1502 Planarity : 0.003 0.051 1531 Dihedral : 5.559 89.928 1251 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1138 helix: 1.82 (0.19), residues: 740 sheet: 0.59 (0.60), residues: 78 loop : -1.92 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 778 HIS 0.004 0.001 HIS B1316 PHE 0.045 0.002 PHE B 433 TYR 0.012 0.001 TYR B 512 ARG 0.003 0.000 ARG B1251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.78 seconds wall clock time: 41 minutes 18.81 seconds (2478.81 seconds total)