Starting phenix.real_space_refine on Wed Mar 12 22:36:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2e_14463/03_2025/7z2e_14463.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2e_14463/03_2025/7z2e_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_14463/03_2025/7z2e_14463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2e_14463/03_2025/7z2e_14463.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2e_14463/03_2025/7z2e_14463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2e_14463/03_2025/7z2e_14463.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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:plan2': 1, ' DA%5*END:plan': 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: 5.12, per 1000 atoms: 0.60 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: 2.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.02 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: 2.73 Time building geometry restraints manager: 2.72 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: 4364 17.79 - 35.57: 565 35.57 - 53.36: 161 53.36 - 71.14: 38 71.14 - 88.93: 14 Dihedral angle restraints: 5142 sinusoidal: 2388 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 5139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1205 0.085 - 0.171: 103 0.171 - 0.256: 1 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 24.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 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 : 0.006 0.204 8772 Z= 0.378 Angle : 0.763 17.151 12063 Z= 0.417 Chirality : 0.047 0.427 1312 Planarity : 0.011 0.341 1396 Dihedral : 17.625 88.931 3366 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 (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: -0.47 (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 TRP 0.014 0.001 TRP B 266 HIS 0.003 0.000 HIS B 208 PHE 0.017 0.001 PHE B 87 TYR 0.014 0.001 TYR A 501 ARG 0.003 0.000 ARG B 356 *********************** 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 : 0.806 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: 0.2020 time to fit residues: 32.8135 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 : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN A 428 GLN A 547 GLN B 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.203022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.167796 restraints weight = 9369.664| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.84 r_work: 0.3582 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8772 Z= 0.251 Angle : 0.577 6.216 12063 Z= 0.298 Chirality : 0.042 0.140 1312 Planarity : 0.005 0.080 1396 Dihedral : 15.416 68.827 1365 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 1.06 % Allowed : 7.80 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.46 (0.28), residues: 933 helix: 1.35 (0.31), residues: 311 sheet: -0.79 (0.39), residues: 158 loop : -1.29 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 406 HIS 0.003 0.001 HIS B 208 PHE 0.018 0.002 PHE B 87 TYR 0.020 0.002 TYR A 501 ARG 0.004 0.000 ARG B 356 *********************** 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 109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.897 Fit side-chains REVERT: A 83 ARG cc_start: 0.5127 (mpt180) cc_final: 0.4769 (mmp80) REVERT: A 256 ASP cc_start: 0.6969 (m-30) cc_final: 0.6688 (m-30) outliers start: 9 outliers final: 7 residues processed: 107 average time/residue: 0.2091 time to fit residues: 31.1886 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 309 ILE 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 9 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 81 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4232 r_free = 0.4232 target = 0.204989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.171584 restraints weight = 9511.666| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.65 r_work: 0.3574 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8772 Z= 0.360 Angle : 0.676 8.103 12063 Z= 0.349 Chirality : 0.046 0.149 1312 Planarity : 0.005 0.072 1396 Dihedral : 15.543 71.722 1365 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 1.77 % Allowed : 13.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.27), residues: 933 helix: 0.66 (0.30), residues: 314 sheet: -1.19 (0.38), residues: 150 loop : -1.60 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 406 HIS 0.004 0.001 HIS A 208 PHE 0.018 0.002 PHE A 171 TYR 0.018 0.002 TYR A 501 ARG 0.005 0.000 ARG B 143 *********************** 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 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.887 Fit side-chains REVERT: A 83 ARG cc_start: 0.5114 (mpt180) cc_final: 0.4730 (mmp80) outliers start: 15 outliers final: 8 residues processed: 107 average time/residue: 0.1803 time to fit residues: 28.3567 Evaluate side-chains 90 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 309 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 39 optimal weight: 0.3980 overall best weight: 1.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 23 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 = 0.4232 r_free = 0.4232 target = 0.206044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.170304 restraints weight = 9359.809| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.68 r_work: 0.3680 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8772 Z= 0.175 Angle : 0.539 7.054 12063 Z= 0.275 Chirality : 0.041 0.231 1312 Planarity : 0.004 0.066 1396 Dihedral : 15.030 68.867 1365 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.00 % Rotamer: Outliers : 2.48 % Allowed : 13.12 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.27), residues: 933 helix: 1.24 (0.31), residues: 316 sheet: -1.06 (0.38), residues: 153 loop : -1.41 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.013 0.001 PHE A 171 TYR 0.018 0.001 TYR B 342 ARG 0.002 0.000 ARG B 358 *********************** 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 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.889 Fit side-chains REVERT: A 83 ARG cc_start: 0.5154 (mpt180) cc_final: 0.4730 (mmp80) REVERT: A 185 ASP cc_start: 0.4873 (OUTLIER) cc_final: 0.4557 (t0) REVERT: A 310 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7446 (mp) REVERT: A 328 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7221 (tt0) REVERT: A 480 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6645 (pt0) REVERT: A 503 LEU cc_start: 0.8065 (tp) cc_final: 0.7784 (mp) REVERT: B 44 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6322 (mt-10) outliers start: 21 outliers final: 7 residues processed: 109 average time/residue: 0.2044 time to fit residues: 32.1082 Evaluate side-chains 96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 95 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.202763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.167140 restraints weight = 9433.275| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.69 r_work: 0.3559 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8772 Z= 0.286 Angle : 0.605 6.777 12063 Z= 0.312 Chirality : 0.043 0.139 1312 Planarity : 0.005 0.061 1396 Dihedral : 15.174 70.363 1365 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 2.36 % Allowed : 14.89 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.27), residues: 933 helix: 0.95 (0.31), residues: 318 sheet: -1.25 (0.37), residues: 153 loop : -1.58 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.013 0.002 PHE B 130 TYR 0.014 0.002 TYR A 457 ARG 0.003 0.000 ARG B 143 *********************** 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 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.937 Fit side-chains REVERT: A 83 ARG cc_start: 0.5144 (mpt180) cc_final: 0.4663 (mmp80) REVERT: A 310 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7416 (mp) REVERT: B 44 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6476 (mt-10) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 0.2521 time to fit residues: 38.4504 Evaluate side-chains 94 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 292 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 505 ILE 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 234 LEU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 8 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 0.0170 chunk 68 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.202770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166979 restraints weight = 9414.747| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.63 r_work: 0.3641 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8772 Z= 0.234 Angle : 0.594 13.365 12063 Z= 0.301 Chirality : 0.043 0.371 1312 Planarity : 0.004 0.057 1396 Dihedral : 15.090 69.975 1365 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 2.48 % Allowed : 15.72 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.94 (0.27), residues: 933 helix: 0.99 (0.31), residues: 318 sheet: -1.23 (0.37), residues: 153 loop : -1.58 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.010 0.001 PHE B 130 TYR 0.015 0.002 TYR A 144 ARG 0.002 0.000 ARG B 143 *********************** 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 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.868 Fit side-chains REVERT: A 83 ARG cc_start: 0.5195 (mpt180) cc_final: 0.4697 (mmp80) REVERT: A 185 ASP cc_start: 0.4851 (OUTLIER) cc_final: 0.4536 (t0) REVERT: A 310 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7440 (mp) REVERT: B 44 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6451 (mt-10) outliers start: 21 outliers final: 13 residues processed: 104 average time/residue: 0.2723 time to fit residues: 41.2005 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 185 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 310 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 202 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.209283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.175017 restraints weight = 9342.026| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.58 r_work: 0.3651 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8772 Z= 0.193 Angle : 0.551 9.511 12063 Z= 0.281 Chirality : 0.042 0.260 1312 Planarity : 0.004 0.058 1396 Dihedral : 14.897 70.109 1365 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 2.60 % Allowed : 16.55 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.27), residues: 933 helix: 1.23 (0.31), residues: 316 sheet: -1.14 (0.37), residues: 153 loop : -1.45 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.009 0.001 PHE A 171 TYR 0.014 0.001 TYR A 144 ARG 0.001 0.000 ARG A 356 *********************** 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 112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.811 Fit side-chains REVERT: A 83 ARG cc_start: 0.5195 (mpt180) cc_final: 0.4713 (mmp80) REVERT: A 202 ILE cc_start: 0.5921 (OUTLIER) cc_final: 0.5687 (mm) REVERT: A 256 ASP cc_start: 0.6735 (m-30) cc_final: 0.6438 (m-30) REVERT: A 310 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7384 (mp) REVERT: A 480 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6305 (pt0) REVERT: B 44 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6262 (mt-10) outliers start: 22 outliers final: 14 residues processed: 106 average time/residue: 0.1848 time to fit residues: 28.3395 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 202 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 542 ILE 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 202 ILE Chi-restraints excluded: chain B residue 234 LEU 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 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.202780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.166832 restraints weight = 9510.121| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.71 r_work: 0.3529 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8772 Z= 0.323 Angle : 0.651 12.255 12063 Z= 0.333 Chirality : 0.045 0.215 1312 Planarity : 0.005 0.057 1396 Dihedral : 15.109 73.382 1365 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.93 % Favored : 94.96 % Rotamer: Outliers : 2.96 % Allowed : 16.90 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.27), residues: 933 helix: 0.71 (0.30), residues: 322 sheet: -1.17 (0.37), residues: 154 loop : -1.65 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 406 HIS 0.003 0.001 HIS A 208 PHE 0.021 0.002 PHE A 171 TYR 0.019 0.002 TYR A 457 ARG 0.004 0.000 ARG B 143 *********************** 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 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.836 Fit side-chains REVERT: A 83 ARG cc_start: 0.5177 (mpt180) cc_final: 0.4651 (mmp80) REVERT: A 310 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7404 (mp) REVERT: A 480 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6352 (pt0) REVERT: B 44 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6427 (mt-10) REVERT: B 287 LYS cc_start: 0.7051 (tttp) cc_final: 0.6073 (mptt) outliers start: 25 outliers final: 18 residues processed: 104 average time/residue: 0.1869 time to fit residues: 27.8942 Evaluate side-chains 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 113 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 TRP Chi-restraints excluded: chain A residue 542 ILE 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 202 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 403 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 85 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.203609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.167179 restraints weight = 9458.912| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.66 r_work: 0.3640 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2069 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= 0.230 Angle : 0.602 13.192 12063 Z= 0.303 Chirality : 0.043 0.357 1312 Planarity : 0.004 0.057 1396 Dihedral : 14.871 71.431 1365 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.18 % Favored : 95.71 % Rotamer: Outliers : 2.36 % Allowed : 17.61 % 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 (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: -0.95 (0.27), residues: 933 helix: 0.89 (0.31), residues: 322 sheet: -1.19 (0.36), residues: 156 loop : -1.55 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.018 0.001 PHE A 171 TYR 0.015 0.002 TYR A 183 ARG 0.002 0.000 ARG B 143 *********************** 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 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.845 Fit side-chains REVERT: A 83 ARG cc_start: 0.5189 (mpt180) cc_final: 0.4586 (mmp80) REVERT: A 310 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7371 (mp) REVERT: A 480 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6363 (pt0) REVERT: B 44 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6371 (mt-10) REVERT: B 287 LYS cc_start: 0.6958 (tttp) cc_final: 0.6026 (mptt) outliers start: 20 outliers final: 17 residues processed: 99 average time/residue: 0.1874 time to fit residues: 26.9261 Evaluate side-chains 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 113 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 5 ILE 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 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 70 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 58 optimal weight: 0.3980 chunk 47 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.206846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.172610 restraints weight = 9383.314| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.58 r_work: 0.3701 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8772 Z= 0.202 Angle : 0.586 14.087 12063 Z= 0.293 Chirality : 0.043 0.366 1312 Planarity : 0.004 0.056 1396 Dihedral : 14.795 70.446 1365 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 2.13 % Allowed : 18.09 % 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 (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: -0.88 (0.27), residues: 933 helix: 1.07 (0.31), residues: 316 sheet: -1.26 (0.37), residues: 153 loop : -1.54 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.019 0.001 PHE A 171 TYR 0.018 0.001 TYR A 183 ARG 0.002 0.000 ARG A 356 ********************** 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 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.857 Fit side-chains REVERT: A 83 ARG cc_start: 0.5188 (mpt180) cc_final: 0.4580 (mmp80) REVERT: A 310 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7465 (mp) REVERT: B 44 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6340 (mt-10) REVERT: B 287 LYS cc_start: 0.6963 (tttp) cc_final: 0.6039 (mptt) outliers start: 18 outliers final: 15 residues processed: 98 average time/residue: 0.1947 time to fit residues: 27.4301 Evaluate side-chains 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 296 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 535 TRP Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 5 ILE 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 42 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.204803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.168250 restraints weight = 9518.520| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.68 r_work: 0.3598 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8772 Z= 0.202 Angle : 0.586 14.087 12063 Z= 0.293 Chirality : 0.043 0.365 1312 Planarity : 0.004 0.056 1396 Dihedral : 14.795 70.446 1365 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 1.89 % Allowed : 18.20 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.88 (0.27), residues: 933 helix: 1.07 (0.31), residues: 316 sheet: -1.26 (0.37), residues: 153 loop : -1.54 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.019 0.001 PHE A 171 TYR 0.018 0.001 TYR A 183 ARG 0.002 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3804.67 seconds wall clock time: 68 minutes 35.03 seconds (4115.03 seconds total)