Starting phenix.real_space_refine on Fri Jul 19 20:25:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/07_2024/7zo9_14844_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/07_2024/7zo9_14844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/07_2024/7zo9_14844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/07_2024/7zo9_14844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/07_2024/7zo9_14844_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zo9_14844/07_2024/7zo9_14844_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 64 atoms to isotropic. 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 V 2 8.30 5 P 4 5.49 5 S 44 5.16 5 C 5526 2.51 5 N 1534 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8730 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4333 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} Conformer: "B" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Conformer: "C" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Chain: "B" Number of atoms: 4333 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} Conformer: "B" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Conformer: "C" Number of residues, atoms: 556, 4317 Classifications: {'peptide': 556} Link IDs: {'PTRANS': 11, 'TRANS': 544} bond proxies already assigned to first conformer: 4380 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.89, per 1000 atoms: 1.48 Number of scatterers: 8730 At special positions: 0 Unit cell: (85.075, 76.875, 131.2, 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) V 2 22.97 S 44 16.00 P 4 15.00 O 1620 8.00 N 1534 7.00 C 5526 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: 3.57 Conformation dependent library (CDL) restraints added in 4.4 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 68.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 4.420A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 46 removed outlier: 4.026A pdb=" N THR A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 56 through 101 removed outlier: 3.593A pdb=" N LEU A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.627A pdb=" N HIS A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 154 removed outlier: 3.881A pdb=" N SER A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 149 - end of helix removed outlier: 3.536A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 203 removed outlier: 3.507A pdb=" N SER A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.660A pdb=" N ALA A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 264 removed outlier: 3.727A pdb=" N LEU A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 314 removed outlier: 3.717A pdb=" N ASP A 274 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.610A pdb=" N ALA A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.610A pdb=" N VAL A 441 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 455 removed outlier: 4.710A pdb=" N PHE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 474 through 489 Processing helix chain 'A' and resid 503 through 519 removed outlier: 3.769A pdb=" N ALA A 513 " --> pdb=" O LYS A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 17 through 46 removed outlier: 4.026A pdb=" N THR B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 56 through 101 removed outlier: 3.592A pdb=" N LEU B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.627A pdb=" N HIS B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 154 removed outlier: 3.880A pdb=" N SER B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Proline residue: B 149 - end of helix removed outlier: 3.537A pdb=" N MET B 154 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 203 removed outlier: 3.507A pdb=" N SER B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LYS B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 213 through 231 removed outlier: 3.661A pdb=" N ALA B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 264 removed outlier: 3.727A pdb=" N LEU B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 314 removed outlier: 3.716A pdb=" N ASP B 274 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 382 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.609A pdb=" N ALA B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 431 Processing helix chain 'B' and resid 437 through 448 removed outlier: 3.612A pdb=" N VAL B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 removed outlier: 4.711A pdb=" N PHE B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 474 through 489 Processing helix chain 'B' and resid 503 through 519 removed outlier: 3.768A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.941A pdb=" N VAL A 340 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA A 389 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 6.589A pdb=" N LEU A 493 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU A 495 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA A 365 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.941A pdb=" N VAL B 340 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA B 389 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 411 through 414 removed outlier: 6.589A pdb=" N LEU B 493 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE B 526 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 495 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA B 365 " --> pdb=" O LEU B 540 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1696 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: 2.36 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2962 1.36 - 1.50: 2174 1.50 - 1.64: 3656 1.64 - 1.77: 0 1.77 - 1.91: 94 Bond restraints: 8886 Sorted by residual: bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" CA PHE A 133 " pdb=" C PHE A 133 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.28e-02 6.10e+03 1.06e+00 bond pdb=" CB PRO A 149 " pdb=" CG PRO A 149 " ideal model delta sigma weight residual 1.492 1.441 0.051 5.00e-02 4.00e+02 1.04e+00 bond pdb=" CB GLN B 512 " pdb=" CG GLN B 512 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 8881 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.80: 179 106.80 - 114.12: 5365 114.12 - 121.44: 4546 121.44 - 128.76: 1908 128.76 - 136.08: 62 Bond angle restraints: 12060 Sorted by residual: angle pdb=" CA GLN A 512 " pdb=" CB GLN A 512 " pdb=" CG GLN A 512 " ideal model delta sigma weight residual 114.10 120.28 -6.18 2.00e+00 2.50e-01 9.55e+00 angle pdb=" CA GLN B 512 " pdb=" CB GLN B 512 " pdb=" CG GLN B 512 " ideal model delta sigma weight residual 114.10 120.27 -6.17 2.00e+00 2.50e-01 9.52e+00 angle pdb=" CB MET B 24 " pdb=" CG MET B 24 " pdb=" SD MET B 24 " ideal model delta sigma weight residual 112.70 121.15 -8.45 3.00e+00 1.11e-01 7.94e+00 angle pdb=" CB MET A 24 " pdb=" CG MET A 24 " pdb=" SD MET A 24 " ideal model delta sigma weight residual 112.70 121.14 -8.44 3.00e+00 1.11e-01 7.92e+00 angle pdb=" CA GLY A 390 " pdb=" C GLY A 390 " pdb=" N ARG A 391 " ideal model delta sigma weight residual 114.75 117.22 -2.47 9.90e-01 1.02e+00 6.21e+00 ... (remaining 12055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 4979 25.74 - 51.49: 297 51.49 - 77.23: 28 77.23 - 102.98: 0 102.98 - 128.72: 4 Dihedral angle restraints: 5308 sinusoidal: 2074 harmonic: 3234 Sorted by residual: dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 171.28 128.72 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual 300.00 171.30 128.70 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 178.78 121.23 1 2.00e+01 2.50e-03 3.64e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 734 0.026 - 0.051: 399 0.051 - 0.077: 186 0.077 - 0.102: 75 0.102 - 0.128: 28 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA ILE A 492 " pdb=" N ILE A 492 " pdb=" C ILE A 492 " pdb=" CB ILE A 492 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE B 492 " pdb=" N ILE B 492 " pdb=" C ILE B 492 " pdb=" CB ILE B 492 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL B 414 " pdb=" N VAL B 414 " pdb=" C VAL B 414 " pdb=" CB VAL B 414 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1419 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 134 " 0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C MET A 134 " -0.058 2.00e-02 2.50e+03 pdb=" O MET A 134 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG A 135 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 134 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C MET B 134 " 0.057 2.00e-02 2.50e+03 pdb=" O MET B 134 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG B 135 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 135 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C ARG B 135 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG B 135 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B 136 " 0.013 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 237 2.71 - 3.26: 9645 3.26 - 3.81: 14346 3.81 - 4.35: 16587 4.35 - 4.90: 27932 Nonbonded interactions: 68747 Sorted by model distance: nonbonded pdb=" O SER B 458 " pdb=" OG1 THR B 463 " model vdw 2.164 2.440 nonbonded pdb=" O SER A 458 " pdb=" OG1 THR A 463 " model vdw 2.165 2.440 nonbonded pdb=" O GLU B 17 " pdb=" OG1 THR B 21 " model vdw 2.246 2.440 nonbonded pdb=" O GLU A 17 " pdb=" OG1 THR A 21 " model vdw 2.247 2.440 nonbonded pdb=" O ILE A 100 " pdb=" NE2 GLN B 209 " model vdw 2.318 2.520 ... (remaining 68742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 251 or resid 253 through 556 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 1 through 251 or resid 253 through 556 or resid 601 throug \ h 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 1.600 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: 0.290 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 37.540 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 0.051 8886 Z= 0.229 Angle : 0.631 8.455 12060 Z= 0.325 Chirality : 0.041 0.128 1422 Planarity : 0.005 0.045 1530 Dihedral : 15.326 128.721 3212 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.13 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 0.40 (0.26), residues: 1112 helix: 1.11 (0.20), residues: 706 sheet: -0.25 (0.56), residues: 80 loop : -1.41 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 8 HIS 0.005 0.001 HIS B 117 PHE 0.027 0.002 PHE B 133 TYR 0.015 0.002 TYR A 169 ARG 0.004 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.962 Fit side-chains REVERT: A 156 MET cc_start: 0.6351 (ptt) cc_final: 0.6052 (ptp) REVERT: B 156 MET cc_start: 0.6389 (ptt) cc_final: 0.6087 (ptp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1660 time to fit residues: 42.4100 Evaluate side-chains 137 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.0170 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 GLN A 283 GLN B 47 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8886 Z= 0.316 Angle : 0.705 8.250 12060 Z= 0.354 Chirality : 0.044 0.188 1422 Planarity : 0.004 0.037 1530 Dihedral : 7.553 99.401 1234 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 2.27 % Allowed : 9.63 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1112 helix: 1.37 (0.19), residues: 718 sheet: -0.16 (0.63), residues: 62 loop : -1.22 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 8 HIS 0.006 0.001 HIS A 191 PHE 0.024 0.002 PHE B 133 TYR 0.027 0.002 TYR B 169 ARG 0.008 0.001 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.044 Fit side-chains REVERT: A 62 TRP cc_start: 0.7140 (t-100) cc_final: 0.6912 (t-100) REVERT: A 121 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7589 (ttp-170) REVERT: A 156 MET cc_start: 0.6756 (ptt) cc_final: 0.6486 (ptp) REVERT: A 167 VAL cc_start: 0.8806 (t) cc_final: 0.8591 (p) REVERT: A 534 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6277 (ptp-170) REVERT: A 541 PHE cc_start: 0.7490 (p90) cc_final: 0.7267 (p90) REVERT: B 156 MET cc_start: 0.6759 (ptt) cc_final: 0.6483 (ptp) REVERT: B 167 VAL cc_start: 0.8817 (t) cc_final: 0.8594 (p) REVERT: B 534 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6293 (ptp-170) REVERT: B 541 PHE cc_start: 0.7467 (p90) cc_final: 0.7250 (p90) outliers start: 21 outliers final: 12 residues processed: 164 average time/residue: 0.1660 time to fit residues: 39.9163 Evaluate side-chains 147 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.0170 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 0.0170 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 283 GLN B 232 GLN B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8886 Z= 0.178 Angle : 0.632 8.911 12060 Z= 0.307 Chirality : 0.042 0.201 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.343 98.039 1234 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % Rotamer: Outliers : 1.30 % Allowed : 12.66 % Favored : 86.04 % 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: 1.08 (0.26), residues: 1112 helix: 1.66 (0.19), residues: 714 sheet: -0.22 (0.58), residues: 62 loop : -1.14 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 62 HIS 0.005 0.001 HIS A 117 PHE 0.024 0.002 PHE B 133 TYR 0.008 0.001 TYR A 169 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 0.925 Fit side-chains REVERT: A 156 MET cc_start: 0.6469 (ptt) cc_final: 0.6198 (ptp) REVERT: A 534 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6319 (ptp-170) REVERT: B 156 MET cc_start: 0.6464 (ptt) cc_final: 0.6185 (ptp) REVERT: B 534 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6317 (ptp-170) outliers start: 12 outliers final: 9 residues processed: 157 average time/residue: 0.1493 time to fit residues: 35.4984 Evaluate side-chains 147 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.0870 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8886 Z= 0.186 Angle : 0.634 9.108 12060 Z= 0.307 Chirality : 0.042 0.190 1422 Planarity : 0.004 0.037 1530 Dihedral : 7.266 98.077 1234 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.87 % Favored : 93.95 % Rotamer: Outliers : 0.87 % Allowed : 15.37 % Favored : 83.77 % 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: 1.02 (0.26), residues: 1112 helix: 1.62 (0.19), residues: 718 sheet: -0.42 (0.57), residues: 60 loop : -1.18 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 62 HIS 0.005 0.001 HIS A 117 PHE 0.023 0.001 PHE B 133 TYR 0.010 0.001 TYR A 169 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 0.985 Fit side-chains REVERT: A 156 MET cc_start: 0.6429 (ptt) cc_final: 0.6170 (ptp) REVERT: A 534 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6252 (ptp-170) REVERT: B 156 MET cc_start: 0.6425 (ptt) cc_final: 0.6162 (ptp) REVERT: B 534 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6280 (ptp-170) outliers start: 8 outliers final: 6 residues processed: 139 average time/residue: 0.1574 time to fit residues: 33.1281 Evaluate side-chains 140 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0770 chunk 60 optimal weight: 0.0270 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8886 Z= 0.161 Angle : 0.630 9.700 12060 Z= 0.301 Chirality : 0.041 0.206 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.183 98.875 1234 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % Rotamer: Outliers : 1.08 % Allowed : 15.04 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1112 helix: 1.84 (0.20), residues: 710 sheet: -0.59 (0.56), residues: 62 loop : -1.16 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 62 HIS 0.006 0.001 HIS B 137 PHE 0.022 0.001 PHE B 133 TYR 0.006 0.001 TYR A 342 ARG 0.005 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.922 Fit side-chains REVERT: A 156 MET cc_start: 0.6377 (ptt) cc_final: 0.6124 (ptp) REVERT: A 534 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.5906 (ptp-170) REVERT: B 156 MET cc_start: 0.6375 (ptt) cc_final: 0.6123 (ptp) REVERT: B 534 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.5965 (ptp-170) outliers start: 10 outliers final: 7 residues processed: 153 average time/residue: 0.1703 time to fit residues: 38.3213 Evaluate side-chains 142 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 534 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 283 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8886 Z= 0.306 Angle : 0.711 8.459 12060 Z= 0.351 Chirality : 0.045 0.182 1422 Planarity : 0.004 0.036 1530 Dihedral : 7.314 99.959 1234 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.78 % Favored : 94.04 % Rotamer: Outliers : 1.84 % Allowed : 16.02 % Favored : 82.14 % 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: 0.70 (0.25), residues: 1112 helix: 1.46 (0.19), residues: 704 sheet: -0.33 (0.56), residues: 62 loop : -1.46 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 8 HIS 0.005 0.001 HIS A 117 PHE 0.028 0.002 PHE B 295 TYR 0.022 0.002 TYR B 169 ARG 0.005 0.001 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.047 Fit side-chains REVERT: A 156 MET cc_start: 0.6757 (ptt) cc_final: 0.6483 (ptp) REVERT: A 541 PHE cc_start: 0.7565 (p90) cc_final: 0.7364 (p90) REVERT: B 156 MET cc_start: 0.6706 (ptt) cc_final: 0.6418 (ptp) outliers start: 17 outliers final: 10 residues processed: 143 average time/residue: 0.1585 time to fit residues: 34.2636 Evaluate side-chains 145 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 148 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8886 Z= 0.171 Angle : 0.637 9.358 12060 Z= 0.306 Chirality : 0.042 0.197 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.226 101.765 1234 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.87 % Favored : 93.95 % Rotamer: Outliers : 0.97 % Allowed : 16.88 % Favored : 82.14 % 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 (0.26), residues: 1112 helix: 1.67 (0.19), residues: 716 sheet: -0.54 (0.55), residues: 60 loop : -1.25 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.005 0.001 HIS B 117 PHE 0.026 0.001 PHE B 295 TYR 0.008 0.001 TYR A 169 ARG 0.004 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 0.998 Fit side-chains REVERT: A 156 MET cc_start: 0.6503 (ptt) cc_final: 0.6256 (ptp) REVERT: A 328 LEU cc_start: 0.8751 (tt) cc_final: 0.8302 (tp) REVERT: B 156 MET cc_start: 0.6559 (ptt) cc_final: 0.6281 (ptp) outliers start: 9 outliers final: 7 residues processed: 148 average time/residue: 0.1713 time to fit residues: 37.4016 Evaluate side-chains 150 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 146 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 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 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8886 Z= 0.175 Angle : 0.652 9.450 12060 Z= 0.308 Chirality : 0.042 0.203 1422 Planarity : 0.004 0.037 1530 Dihedral : 7.174 104.086 1234 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.78 % Favored : 94.04 % Rotamer: Outliers : 1.08 % Allowed : 17.21 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1112 helix: 1.70 (0.19), residues: 718 sheet: -0.50 (0.55), residues: 60 loop : -1.17 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.005 0.001 HIS A 117 PHE 0.028 0.001 PHE B 295 TYR 0.014 0.001 TYR B 263 ARG 0.004 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 0.973 Fit side-chains REVERT: A 7 TYR cc_start: 0.8559 (m-10) cc_final: 0.8342 (m-10) REVERT: A 156 MET cc_start: 0.6467 (ptt) cc_final: 0.6172 (ptp) REVERT: B 156 MET cc_start: 0.6453 (ptt) cc_final: 0.6172 (ptp) outliers start: 10 outliers final: 10 residues processed: 149 average time/residue: 0.1571 time to fit residues: 35.8262 Evaluate side-chains 149 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.0050 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 104 optimal weight: 0.0060 chunk 63 optimal weight: 0.9990 overall best weight: 0.1366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8886 Z= 0.151 Angle : 0.652 10.485 12060 Z= 0.302 Chirality : 0.042 0.201 1422 Planarity : 0.004 0.039 1530 Dihedral : 7.092 105.460 1234 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.23 % Favored : 94.58 % Rotamer: Outliers : 0.65 % Allowed : 18.29 % Favored : 81.06 % 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: 1.30 (0.26), residues: 1112 helix: 1.96 (0.20), residues: 706 sheet: -0.43 (0.54), residues: 72 loop : -1.28 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.005 0.001 HIS A 117 PHE 0.021 0.001 PHE B 295 TYR 0.014 0.001 TYR A 263 ARG 0.004 0.000 ARG B 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.8902 (mm) cc_final: 0.8282 (mp) REVERT: A 156 MET cc_start: 0.6421 (ptt) cc_final: 0.5915 (ttp) REVERT: B 156 MET cc_start: 0.6218 (ptt) cc_final: 0.5919 (ptp) REVERT: B 328 LEU cc_start: 0.8698 (tt) cc_final: 0.8281 (tp) REVERT: B 541 PHE cc_start: 0.7331 (p90) cc_final: 0.6796 (p90) outliers start: 6 outliers final: 6 residues processed: 163 average time/residue: 0.1629 time to fit residues: 39.3554 Evaluate side-chains 151 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 109 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8886 Z= 0.170 Angle : 0.657 12.528 12060 Z= 0.309 Chirality : 0.042 0.184 1422 Planarity : 0.004 0.038 1530 Dihedral : 7.103 107.425 1234 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.69 % Favored : 94.13 % Rotamer: Outliers : 0.54 % Allowed : 20.45 % Favored : 79.00 % 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: 1.18 (0.26), residues: 1112 helix: 1.83 (0.19), residues: 708 sheet: -0.32 (0.55), residues: 70 loop : -1.30 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.005 0.001 HIS A 117 PHE 0.029 0.002 PHE B 295 TYR 0.014 0.001 TYR B 263 ARG 0.004 0.000 ARG A 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.8909 (mm) cc_final: 0.8317 (mp) REVERT: A 156 MET cc_start: 0.6396 (ptt) cc_final: 0.5894 (ttp) REVERT: B 156 MET cc_start: 0.6335 (ptt) cc_final: 0.6012 (ptp) REVERT: B 328 LEU cc_start: 0.8700 (tt) cc_final: 0.8260 (tp) outliers start: 5 outliers final: 5 residues processed: 150 average time/residue: 0.1730 time to fit residues: 38.2834 Evaluate side-chains 147 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0000 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.155561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.124242 restraints weight = 107515.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.131134 restraints weight = 22418.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.135752 restraints weight = 9934.743| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8886 Z= 0.182 Angle : 0.671 12.322 12060 Z= 0.313 Chirality : 0.042 0.181 1422 Planarity : 0.004 0.037 1530 Dihedral : 7.108 108.755 1234 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.23 % Favored : 93.59 % Rotamer: Outliers : 0.65 % Allowed : 20.67 % Favored : 78.68 % 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: 1.19 (0.26), residues: 1112 helix: 1.79 (0.19), residues: 712 sheet: -0.23 (0.55), residues: 70 loop : -1.21 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 106 HIS 0.005 0.001 HIS A 117 PHE 0.029 0.002 PHE B 295 TYR 0.015 0.001 TYR B 263 ARG 0.004 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.09 seconds wall clock time: 35 minutes 8.12 seconds (2108.12 seconds total)