Starting phenix.real_space_refine on Fri Sep 11 07:06:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z2e_14463/09_2026/7z2e_14463.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2e_14463/09_2026/7z2e_14463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2e_14463/09_2026/7z2e_14463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2e_14463/09_2026/7z2e_14463.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2e_14463/09_2026/7z2e_14463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2e_14463/09_2026/7z2e_14463.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z2e_14463/09_2026/7z2e_14463.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z2e_14463/09_2026/7z2e_14463.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 12 5.16 5 C 5380 2.51 5 N 1418 2.21 5 O 1634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8479 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4331 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 496} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3399 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 381} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 721 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'T27': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.88, per 1000 atoms: 0.22 Number of scatterers: 8479 At special positions: 0 Unit cell: (97.97, 112.52, 101.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 35 15.00 O 1634 8.00 N 1418 7.00 C 5380 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 - 3.00 Amino acid : True - 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: 0.91 Conformation dependent library (CDL) restraints added in 337.9 milliseconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 37.8% alpha, 13.3% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 77 through 82 removed outlier: 4.007A pdb=" N LYS A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.585A pdb=" N TYR A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.791A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 removed outlier: 4.006A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.704A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.569A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.602A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.535A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.577A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 4.239A pdb=" N ALA A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.854A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 removed outlier: 3.574A pdb=" N LYS B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.804A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.639A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.170A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 213 removed outlier: 3.580A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.627A pdb=" N LYS B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 296 through 311 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 removed outlier: 4.041A pdb=" N SER A 48 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 145 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.511A pdb=" N PHE A 227 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 354 removed outlier: 7.478A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 464 through 468 removed outlier: 3.887A pdb=" N VAL A 467 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 455 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AA9, first strand: chain 'B' and resid 350 through 355 removed outlier: 3.925A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1319 1.27 - 1.40: 2160 1.40 - 1.54: 5031 1.54 - 1.67: 240 1.67 - 1.81: 22 Bond restraints: 8772 Sorted by residual: bond pdb=" CG PRO B 345 " pdb=" CD PRO B 345 " ideal model delta sigma weight residual 1.503 1.299 0.204 3.40e-02 8.65e+02 3.60e+01 bond pdb=" C13 T27 A 601 " pdb=" C19 T27 A 601 " ideal model delta sigma weight residual 1.422 1.530 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" CA THR B 419 " pdb=" C THR B 419 " ideal model delta sigma weight residual 1.524 1.591 -0.067 1.26e-02 6.30e+03 2.83e+01 bond pdb=" C20 T27 A 601 " pdb=" C22 T27 A 601 " ideal model delta sigma weight residual 1.419 1.525 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C THR B 419 " pdb=" N PRO B 420 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.18e-02 7.18e+03 2.63e+01 ... (remaining 8767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 11978 3.43 - 6.86: 71 6.86 - 10.29: 9 10.29 - 13.72: 1 13.72 - 17.15: 4 Bond angle restraints: 12063 Sorted by residual: angle pdb=" CA PRO B 345 " pdb=" N PRO B 345 " pdb=" CD PRO B 345 " ideal model delta sigma weight residual 112.00 94.85 17.15 1.40e+00 5.10e-01 1.50e+02 angle pdb=" N ASN B 418 " pdb=" CA ASN B 418 " pdb=" C ASN B 418 " ideal model delta sigma weight residual 107.75 90.82 16.93 1.86e+00 2.89e-01 8.28e+01 angle pdb=" N PRO B 345 " pdb=" CD PRO B 345 " pdb=" CG PRO B 345 " ideal model delta sigma weight residual 103.20 91.18 12.02 1.50e+00 4.44e-01 6.42e+01 angle pdb=" C2 T27 A 601 " pdb=" C1 T27 A 601 " pdb=" C7 T27 A 601 " ideal model delta sigma weight residual 120.40 104.25 16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" C PRO B 140 " pdb=" CA PRO B 140 " pdb=" CB PRO B 140 " ideal model delta sigma weight residual 111.56 102.70 8.86 1.65e+00 3.67e-01 2.88e+01 ... (remaining 12058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4363 17.79 - 35.57: 565 35.57 - 53.36: 161 53.36 - 71.14: 38 71.14 - 88.93: 14 Dihedral angle restraints: 5141 sinusoidal: 2387 harmonic: 2754 Sorted by residual: dihedral pdb=" C ILE A 184 " pdb=" N ILE A 184 " pdb=" CA ILE A 184 " pdb=" CB ILE A 184 " ideal model delta harmonic sigma weight residual -122.00 -137.20 15.20 0 2.50e+00 1.60e-01 3.70e+01 dihedral pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CA ILE A 184 " pdb=" CB ILE A 184 " ideal model delta harmonic sigma weight residual 123.40 136.42 -13.02 0 2.50e+00 1.60e-01 2.71e+01 dihedral pdb=" CD ARG B 143 " pdb=" NE ARG B 143 " pdb=" CZ ARG B 143 " pdb=" NH1 ARG B 143 " ideal model delta sinusoidal sigma weight residual 0.00 44.11 -44.11 1 1.00e+01 1.00e-02 2.71e+01 ... (remaining 5138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1197 0.085 - 0.171: 108 0.171 - 0.256: 4 0.256 - 0.341: 1 0.341 - 0.427: 2 Chirality restraints: 1312 Sorted by residual: chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.01 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA THR B 419 " pdb=" N THR B 419 " pdb=" C THR B 419 " pdb=" CB THR B 419 " both_signs ideal model delta sigma weight residual False 2.53 2.87 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ASN B 418 " pdb=" N ASN B 418 " pdb=" C ASN B 418 " pdb=" CB ASN B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 1309 not shown) Planarity restraints: 1396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 143 " 0.761 9.50e-02 1.11e+02 3.41e-01 7.08e+01 pdb=" NE ARG B 143 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 143 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 143 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 143 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 344 " -0.096 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO B 345 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO B 345 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 345 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 467 " -0.079 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO A 468 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.061 5.00e-02 4.00e+02 ... (remaining 1393 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1205 2.76 - 3.30: 7556 3.30 - 3.83: 13994 3.83 - 4.37: 16361 4.37 - 4.90: 27363 Nonbonded interactions: 66479 Sorted by model distance: nonbonded pdb=" OH TYR A 354 " pdb=" OE1 GLU A 370 " model vdw 2.227 3.040 nonbonded pdb=" NZ LYS B 73 " pdb=" OH TYR B 146 " model vdw 2.249 3.120 nonbonded pdb=" OG1 THR A 27 " pdb=" O LYS A 30 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR A 253 " pdb=" OD2 ASP A 256 " model vdw 2.284 3.040 nonbonded pdb=" OD1 ASP A 443 " pdb=" N GLY A 444 " model vdw 2.291 3.120 ... (remaining 66474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 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 : 0.005 0.204 8772 Z= 0.261 Angle : 0.750 17.151 12063 Z= 0.424 Chirality : 0.048 0.427 1312 Planarity : 0.011 0.341 1396 Dihedral : 17.627 88.931 3365 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 0.24 % Allowed : 0.83 % Favored : 98.94 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.28), residues: 933 helix: 1.33 (0.31), residues: 311 sheet: -0.70 (0.40), residues: 161 loop : -1.34 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.014 0.001 TYR A 501 PHE 0.017 0.001 PHE B 87 TRP 0.014 0.001 TRP B 266 HIS 0.003 0.000 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 ( 8772) covalent geometry : angle 0.75002 / 0.42 (12063) hydrogen bonds : bond 0.13490 / 8.36 ( 333) hydrogen bonds : angle 6.54242 / 4.49 ( 897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.302 Fit side-chains REVERT: A 115 TYR cc_start: 0.6802 (t80) cc_final: 0.6540 (t80) REVERT: A 233 GLU cc_start: 0.7266 (mp0) cc_final: 0.6986 (mp0) outliers start: 2 outliers final: 0 residues processed: 117 average time/residue: 0.0800 time to fit residues: 13.3265 Evaluate side-chains 86 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN A 547 GLN B 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.213036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.181134 restraints weight = 9426.538| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.56 r_work: 0.3747 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8772 Z= 0.139 Angle : 0.571 7.311 12063 Z= 0.303 Chirality : 0.044 0.182 1312 Planarity : 0.005 0.079 1396 Dihedral : 15.434 71.026 1364 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 0.83 % Allowed : 6.62 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.28), residues: 933 helix: 1.42 (0.31), residues: 311 sheet: -0.52 (0.40), residues: 154 loop : -1.29 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.021 0.001 TYR A 501 PHE 0.020 0.001 PHE B 87 TRP 0.020 0.001 TRP A 406 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8772) covalent geometry : angle 0.57089 / 0.30 (12063) hydrogen bonds : bond 0.04143 / 2.63 ( 333) hydrogen bonds : angle 4.40820 / 2.97 ( 897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.272 Fit side-chains REVERT: A 83 ARG cc_start: 0.5092 (mpt180) cc_final: 0.4734 (mmp80) REVERT: A 115 TYR cc_start: 0.6751 (t80) cc_final: 0.6357 (t80) REVERT: A 256 ASP cc_start: 0.6855 (m-30) cc_final: 0.6603 (m-30) outliers start: 7 outliers final: 4 residues processed: 108 average time/residue: 0.0902 time to fit residues: 13.5255 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 531 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN B 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.213873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.182559 restraints weight = 9372.778| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.47 r_work: 0.3698 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8772 Z= 0.158 Angle : 0.580 7.470 12063 Z= 0.303 Chirality : 0.044 0.144 1312 Planarity : 0.005 0.068 1396 Dihedral : 15.385 68.283 1364 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 1.42 % Allowed : 10.52 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.28), residues: 933 helix: 1.31 (0.31), residues: 312 sheet: -0.85 (0.39), residues: 153 loop : -1.39 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 TYR 0.022 0.002 TYR A 501 PHE 0.021 0.002 PHE A 171 TRP 0.030 0.002 TRP A 406 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8772) covalent geometry : angle 0.57972 / 0.30 (12063) hydrogen bonds : bond 0.03993 / 2.56 ( 333) hydrogen bonds : angle 4.37542 / 2.98 ( 897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.203 Fit side-chains REVERT: A 83 ARG cc_start: 0.5086 (mpt180) cc_final: 0.4661 (mmp80) REVERT: A 480 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6626 (pt0) outliers start: 12 outliers final: 6 residues processed: 108 average time/residue: 0.0785 time to fit residues: 11.9828 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 531 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 83 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 81 optimal weight: 40.0000 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 68 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.204013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.169816 restraints weight = 9528.653| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.66 r_work: 0.3609 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8772 Z= 0.196 Angle : 0.631 8.492 12063 Z= 0.328 Chirality : 0.047 0.327 1312 Planarity : 0.005 0.060 1396 Dihedral : 15.404 69.591 1364 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 2.72 % Allowed : 12.53 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.27), residues: 933 helix: 0.93 (0.30), residues: 318 sheet: -1.16 (0.38), residues: 152 loop : -1.56 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.017 0.002 TYR A 339 PHE 0.014 0.002 PHE B 130 TRP 0.034 0.002 TRP A 406 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 8772) covalent geometry : angle 0.63141 / 0.33 (12063) hydrogen bonds : bond 0.04268 / 2.78 ( 333) hydrogen bonds : angle 4.54230 / 3.13 ( 897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.303 Fit side-chains REVERT: A 83 ARG cc_start: 0.5142 (mpt180) cc_final: 0.4702 (mmp80) REVERT: A 256 ASP cc_start: 0.6867 (m-30) cc_final: 0.6636 (m-30) REVERT: A 503 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7713 (mp) REVERT: B 44 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6489 (mt-10) outliers start: 23 outliers final: 11 residues processed: 113 average time/residue: 0.0740 time to fit residues: 12.0662 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 25 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 chunk 96 optimal weight: 50.0000 chunk 9 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.209165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.175152 restraints weight = 9411.895| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.73 r_work: 0.3627 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8772 Z= 0.124 Angle : 0.554 7.078 12063 Z= 0.289 Chirality : 0.043 0.180 1312 Planarity : 0.004 0.054 1396 Dihedral : 15.246 69.833 1364 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.75 % Favored : 96.14 % Rotamer: Outliers : 1.42 % Allowed : 13.83 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.27), residues: 933 helix: 1.28 (0.31), residues: 316 sheet: -1.04 (0.38), residues: 153 loop : -1.44 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 356 TYR 0.013 0.001 TYR A 144 PHE 0.010 0.001 PHE A 171 TRP 0.032 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8772) covalent geometry : angle 0.55378 / 0.29 (12063) hydrogen bonds : bond 0.03580 / 2.34 ( 333) hydrogen bonds : angle 4.35316 / 2.98 ( 897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.327 Fit side-chains REVERT: A 83 ARG cc_start: 0.5217 (mpt180) cc_final: 0.4821 (mmp80) REVERT: A 480 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6339 (pt0) REVERT: A 503 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7654 (mp) REVERT: B 44 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6348 (mt-10) outliers start: 12 outliers final: 7 residues processed: 105 average time/residue: 0.0983 time to fit residues: 14.5084 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 31 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 0.0370 chunk 83 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 overall best weight: 3.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.204224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.169786 restraints weight = 9467.830| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.68 r_work: 0.3636 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8772 Z= 0.162 Angle : 0.591 12.052 12063 Z= 0.306 Chirality : 0.045 0.428 1312 Planarity : 0.004 0.052 1396 Dihedral : 15.218 70.282 1364 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 1.89 % Allowed : 15.13 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.27), residues: 933 helix: 1.12 (0.30), residues: 318 sheet: -1.15 (0.37), residues: 153 loop : -1.49 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.021 0.002 TYR A 501 PHE 0.012 0.001 PHE B 130 TRP 0.032 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 8772) covalent geometry : angle 0.59139 / 0.31 (12063) hydrogen bonds : bond 0.03879 / 2.51 ( 333) hydrogen bonds : angle 4.41607 / 3.03 ( 897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.324 Fit side-chains REVERT: A 83 ARG cc_start: 0.5169 (mpt180) cc_final: 0.4745 (mmp80) REVERT: A 480 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6382 (pt0) REVERT: A 503 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7727 (mp) REVERT: A 530 LYS cc_start: 0.7096 (mmtp) cc_final: 0.6811 (mmtp) REVERT: B 44 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6347 (mt-10) outliers start: 16 outliers final: 10 residues processed: 100 average time/residue: 0.0946 time to fit residues: 13.2850 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN B 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.201657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.168074 restraints weight = 9620.931| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.69 r_work: 0.3575 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8772 Z= 0.240 Angle : 0.702 9.453 12063 Z= 0.363 Chirality : 0.048 0.278 1312 Planarity : 0.005 0.051 1396 Dihedral : 15.406 70.978 1364 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.79 % Favored : 94.11 % Rotamer: Outliers : 2.84 % Allowed : 16.19 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.27), residues: 933 helix: 0.53 (0.30), residues: 324 sheet: -1.23 (0.37), residues: 153 loop : -1.73 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 143 TYR 0.018 0.003 TYR A 339 PHE 0.017 0.002 PHE B 130 TRP 0.034 0.003 TRP A 406 HIS 0.004 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 ( 8772) covalent geometry : angle 0.70238 / 0.36 (12063) hydrogen bonds : bond 0.04812 / 3.11 ( 333) hydrogen bonds : angle 4.78886 / 3.31 ( 897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.329 Fit side-chains REVERT: A 83 ARG cc_start: 0.5153 (mpt180) cc_final: 0.4717 (mmp80) REVERT: A 503 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7792 (mp) REVERT: A 530 LYS cc_start: 0.7289 (mmtp) cc_final: 0.6983 (mmtp) REVERT: B 287 LYS cc_start: 0.7075 (tttp) cc_final: 0.6111 (mptt) outliers start: 24 outliers final: 13 residues processed: 110 average time/residue: 0.0786 time to fit residues: 12.6039 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.206086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.171215 restraints weight = 9399.100| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.59 r_work: 0.3680 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8772 Z= 0.118 Angle : 0.559 8.796 12063 Z= 0.292 Chirality : 0.042 0.242 1312 Planarity : 0.004 0.051 1396 Dihedral : 15.093 70.416 1364 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.79 % Favored : 97.11 % Rotamer: Outliers : 1.54 % Allowed : 17.26 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.27), residues: 933 helix: 1.16 (0.31), residues: 316 sheet: -1.28 (0.36), residues: 153 loop : -1.51 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.016 0.001 TYR A 144 PHE 0.010 0.001 PHE A 171 TRP 0.042 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 8772) covalent geometry : angle 0.55910 / 0.29 (12063) hydrogen bonds : bond 0.03452 / 2.26 ( 333) hydrogen bonds : angle 4.39475 / 3.00 ( 897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.318 Fit side-chains REVERT: A 83 ARG cc_start: 0.5122 (mpt180) cc_final: 0.4725 (mmp80) REVERT: A 310 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7502 (mp) REVERT: A 480 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6148 (pt0) REVERT: A 503 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7715 (mp) REVERT: A 530 LYS cc_start: 0.7186 (mmtp) cc_final: 0.6887 (mmtp) REVERT: B 44 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6351 (mt-10) outliers start: 13 outliers final: 7 residues processed: 107 average time/residue: 0.0913 time to fit residues: 13.8135 Evaluate side-chains 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 370 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 90 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.202872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166801 restraints weight = 9488.901| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.65 r_work: 0.3591 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8772 Z= 0.173 Angle : 0.610 7.349 12063 Z= 0.318 Chirality : 0.044 0.244 1312 Planarity : 0.005 0.050 1396 Dihedral : 15.096 70.796 1364 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 1.65 % Allowed : 17.97 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.27), residues: 933 helix: 0.93 (0.31), residues: 316 sheet: -1.33 (0.36), residues: 153 loop : -1.58 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.042 0.002 TYR A 501 PHE 0.021 0.002 PHE A 171 TRP 0.039 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 8772) covalent geometry : angle 0.61007 / 0.32 (12063) hydrogen bonds : bond 0.03936 / 2.56 ( 333) hydrogen bonds : angle 4.58359 / 3.12 ( 897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.224 Fit side-chains REVERT: A 83 ARG cc_start: 0.5125 (mpt180) cc_final: 0.4724 (mmp80) REVERT: A 310 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7452 (mp) REVERT: A 480 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6293 (pt0) REVERT: A 503 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7741 (mp) REVERT: A 530 LYS cc_start: 0.7240 (mmtp) cc_final: 0.6935 (mmtp) REVERT: B 44 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6413 (mt-10) REVERT: B 287 LYS cc_start: 0.6999 (tttp) cc_final: 0.6048 (mptt) outliers start: 14 outliers final: 10 residues processed: 99 average time/residue: 0.0904 time to fit residues: 12.6891 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 71 optimal weight: 0.0060 chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 36 optimal weight: 0.1980 chunk 81 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 48 optimal weight: 0.0070 chunk 63 optimal weight: 0.9980 overall best weight: 0.6416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.207185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.172186 restraints weight = 9415.075| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.61 r_work: 0.3671 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8772 Z= 0.111 Angle : 0.545 7.302 12063 Z= 0.284 Chirality : 0.041 0.227 1312 Planarity : 0.004 0.052 1396 Dihedral : 14.940 70.863 1364 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Rotamer: Outliers : 1.30 % Allowed : 18.68 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.27), residues: 933 helix: 1.30 (0.31), residues: 316 sheet: -0.93 (0.37), residues: 153 loop : -1.42 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 TYR 0.039 0.001 TYR A 501 PHE 0.018 0.001 PHE A 171 TRP 0.046 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8772) covalent geometry : angle 0.54468 / 0.28 (12063) hydrogen bonds : bond 0.03151 / 2.08 ( 333) hydrogen bonds : angle 4.33094 / 2.92 ( 897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.301 Fit side-chains REVERT: A 83 ARG cc_start: 0.5136 (mpt180) cc_final: 0.4750 (mmp80) REVERT: A 310 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7446 (mp) REVERT: A 503 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7729 (mp) REVERT: A 530 LYS cc_start: 0.7127 (mmtp) cc_final: 0.6831 (mmtp) REVERT: B 44 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6286 (mt-10) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.0898 time to fit residues: 13.0085 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 96 optimal weight: 50.0000 chunk 7 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN A 480 GLN A 547 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.204284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.170320 restraints weight = 9339.704| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.53 r_work: 0.3601 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8772 Z= 0.246 Angle : 0.707 14.064 12063 Z= 0.361 Chirality : 0.048 0.334 1312 Planarity : 0.005 0.051 1396 Dihedral : 15.114 71.052 1364 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.25 % Favored : 94.64 % Rotamer: Outliers : 1.54 % Allowed : 18.68 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.27), residues: 933 helix: 0.63 (0.30), residues: 324 sheet: -1.36 (0.37), residues: 151 loop : -1.68 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 143 TYR 0.044 0.003 TYR A 501 PHE 0.018 0.002 PHE B 130 TRP 0.036 0.003 TRP A 406 HIS 0.004 0.001 HIS A 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 ( 8772) covalent geometry : angle 0.70688 / 0.36 (12063) hydrogen bonds : bond 0.04592 / 2.99 ( 333) hydrogen bonds : angle 4.78669 / 3.27 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.89 seconds wall clock time: 31 minutes 45.12 seconds (1905.12 seconds total)