Starting phenix.real_space_refine on Wed Feb 12 21:31:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2e_14463/02_2025/7z2e_14463.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2e_14463/02_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_14463/02_2025/7z2e_14463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2e_14463/02_2025/7z2e_14463.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2e_14463/02_2025/7z2e_14463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2e_14463/02_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-5592/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: 4.96, per 1000 atoms: 0.58 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: 2.27 Conformation dependent library (CDL) restraints added in 832.1 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: 2.43 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: 2.51 Time building geometry restraints manager: 2.57 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: 0.100 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.170 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- 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 : 0.823 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: 0.2075 time to fit residues: 33.8117 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 : 0.867 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.209966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.177731 restraints weight = 9373.370| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.56 r_work: 0.3694 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8772 Z= 0.255 Angle : 0.581 5.905 12063 Z= 0.299 Chirality : 0.042 0.139 1312 Planarity : 0.005 0.080 1396 Dihedral : 15.415 68.278 1365 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.06 % Allowed : 7.92 % Favored : 91.02 % 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: -0.46 (0.28), residues: 933 helix: 1.36 (0.31), residues: 311 sheet: -0.80 (0.39), residues: 158 loop : -1.29 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 406 HIS 0.003 0.001 HIS B 208 PHE 0.017 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 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.981 Fit side-chains REVERT: A 83 ARG cc_start: 0.5168 (mpt180) cc_final: 0.4815 (mmp80) REVERT: A 256 ASP cc_start: 0.7077 (m-30) cc_final: 0.6806 (m-30) outliers start: 9 outliers final: 7 residues processed: 108 average time/residue: 0.2210 time to fit residues: 33.1480 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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: 6.9990 chunk 45 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 55 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 81 optimal weight: 40.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.205567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.172097 restraints weight = 9506.062| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.66 r_work: 0.3707 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8772 Z= 0.274 Angle : 0.594 6.063 12063 Z= 0.307 Chirality : 0.043 0.143 1312 Planarity : 0.005 0.070 1396 Dihedral : 15.312 69.373 1365 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 2.13 % Allowed : 12.17 % Favored : 85.70 % 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: -0.78 (0.27), residues: 933 helix: 1.03 (0.30), residues: 318 sheet: -1.03 (0.38), residues: 152 loop : -1.45 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 406 HIS 0.003 0.001 HIS A 208 PHE 0.019 0.002 PHE A 171 TYR 0.015 0.002 TYR A 501 ARG 0.003 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 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.5192 (mpt180) cc_final: 0.4792 (mmp80) REVERT: B 44 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6356 (mt-10) outliers start: 18 outliers final: 8 residues processed: 110 average time/residue: 0.2111 time to fit residues: 32.4901 Evaluate side-chains 96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 403 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.207273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.173463 restraints weight = 9306.981| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.57 r_work: 0.3698 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8772 Z= 0.238 Angle : 0.581 8.401 12063 Z= 0.297 Chirality : 0.043 0.291 1312 Planarity : 0.005 0.065 1396 Dihedral : 15.150 69.303 1365 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 2.25 % Allowed : 13.12 % Favored : 84.63 % 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: -0.77 (0.27), residues: 933 helix: 1.06 (0.31), residues: 318 sheet: -1.12 (0.37), residues: 152 loop : -1.43 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 406 HIS 0.002 0.001 HIS A 198 PHE 0.012 0.001 PHE A 171 TYR 0.014 0.002 TYR A 144 ARG 0.002 0.000 ARG B 143 *********************** 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 111 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.5184 (mpt180) cc_final: 0.4765 (mmp80) REVERT: A 185 ASP cc_start: 0.4933 (OUTLIER) cc_final: 0.4577 (t0) REVERT: A 256 ASP cc_start: 0.7078 (m-30) cc_final: 0.6873 (m-30) REVERT: A 503 LEU cc_start: 0.8079 (tp) cc_final: 0.7787 (mp) REVERT: B 44 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6431 (mt-10) outliers start: 19 outliers final: 13 residues processed: 107 average time/residue: 0.1984 time to fit residues: 30.2223 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 : 0.871 ------------------------------------------------------------------------------- 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 185 ASP Chi-restraints excluded: chain A residue 296 THR 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 10 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 403 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 95 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 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 = 0.4195 r_free = 0.4195 target = 0.201548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.166057 restraints weight = 9468.231| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.65 r_work: 0.3630 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8772 Z= 0.362 Angle : 0.668 7.897 12063 Z= 0.344 Chirality : 0.045 0.182 1312 Planarity : 0.005 0.063 1396 Dihedral : 15.341 71.897 1365 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 2.96 % Allowed : 14.54 % Favored : 82.51 % 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: -1.19 (0.27), residues: 933 helix: 0.60 (0.30), residues: 320 sheet: -1.25 (0.37), residues: 153 loop : -1.63 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 406 HIS 0.003 0.001 HIS A 208 PHE 0.014 0.002 PHE B 130 TYR 0.017 0.002 TYR A 457 ARG 0.004 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 119 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.5050 (mpt180) cc_final: 0.4653 (mmp80) REVERT: A 310 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7450 (mp) REVERT: B 287 LYS cc_start: 0.7080 (tttp) cc_final: 0.6079 (mptt) outliers start: 25 outliers final: 15 residues processed: 115 average time/residue: 0.1967 time to fit residues: 32.4054 Evaluate side-chains 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 8 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 68 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 = 0.4212 r_free = 0.4212 target = 0.203424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.167447 restraints weight = 9401.566| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.64 r_work: 0.3591 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8772 Z= 0.253 Angle : 0.604 11.382 12063 Z= 0.307 Chirality : 0.043 0.324 1312 Planarity : 0.005 0.060 1396 Dihedral : 15.108 70.356 1365 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 2.96 % Allowed : 16.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.27), residues: 933 helix: 0.90 (0.31), residues: 314 sheet: -1.35 (0.37), residues: 152 loop : -1.58 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.019 0.002 PHE A 171 TYR 0.016 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 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.988 Fit side-chains REVERT: A 83 ARG cc_start: 0.5194 (mpt180) cc_final: 0.4739 (mmp80) REVERT: A 202 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5750 (mm) REVERT: A 310 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7396 (mp) REVERT: A 480 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6148 (pt0) REVERT: B 44 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6929 (mm-30) REVERT: B 287 LYS cc_start: 0.7037 (tttp) cc_final: 0.6084 (mptt) outliers start: 25 outliers final: 17 residues processed: 110 average time/residue: 0.2078 time to fit residues: 32.3321 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 : 1.058 ------------------------------------------------------------------------------- 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 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 351 THR 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 234 LEU Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 403 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 93 optimal weight: 0.0050 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.203905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.167935 restraints weight = 9436.089| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.64 r_work: 0.3595 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8772 Z= 0.245 Angle : 0.588 9.062 12063 Z= 0.301 Chirality : 0.043 0.232 1312 Planarity : 0.005 0.059 1396 Dihedral : 14.973 70.657 1365 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 3.07 % Allowed : 16.67 % Favored : 80.26 % 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: -1.01 (0.27), residues: 933 helix: 0.92 (0.31), residues: 316 sheet: -1.33 (0.36), residues: 152 loop : -1.58 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.017 0.001 PHE A 171 TYR 0.015 0.002 TYR A 144 ARG 0.002 0.000 ARG B 143 *********************** 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: 26 poor density : 90 time to evaluate : 0.931 Fit side-chains REVERT: A 83 ARG cc_start: 0.5244 (mpt180) cc_final: 0.4739 (mmp80) REVERT: A 202 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5601 (mm) REVERT: A 310 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7408 (mp) REVERT: A 480 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6316 (pt0) REVERT: B 44 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6823 (mm-30) REVERT: B 287 LYS cc_start: 0.7021 (tttp) cc_final: 0.6080 (mptt) outliers start: 26 outliers final: 20 residues processed: 111 average time/residue: 0.1975 time to fit residues: 31.6610 Evaluate side-chains 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 351 THR Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 505 ILE 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 369 THR Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 403 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.203750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.168079 restraints weight = 9466.282| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.62 r_work: 0.3659 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8772 Z= 0.279 Angle : 0.634 13.463 12063 Z= 0.320 Chirality : 0.044 0.367 1312 Planarity : 0.005 0.057 1396 Dihedral : 14.991 72.610 1365 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 2.96 % Allowed : 17.73 % Favored : 79.31 % 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: 0.74 (0.30), residues: 320 sheet: -1.38 (0.37), residues: 152 loop : -1.59 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.020 0.002 PHE A 171 TYR 0.018 0.002 TYR A 457 ARG 0.003 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 114 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.831 Fit side-chains REVERT: A 83 ARG cc_start: 0.5227 (mpt180) cc_final: 0.4749 (mmp80) REVERT: A 310 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7345 (mp) REVERT: A 480 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6422 (pt0) REVERT: B 44 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6828 (mm-30) REVERT: B 287 LYS cc_start: 0.7048 (tttp) cc_final: 0.6118 (mptt) outliers start: 25 outliers final: 20 residues processed: 110 average time/residue: 0.1904 time to fit residues: 29.9855 Evaluate side-chains 109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 369 THR Chi-restraints excluded: chain B residue 370 GLU 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: 10.0000 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.202641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.166959 restraints weight = 9456.359| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.63 r_work: 0.3663 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2162 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= 0.243 Angle : 0.608 12.970 12063 Z= 0.307 Chirality : 0.043 0.365 1312 Planarity : 0.005 0.057 1396 Dihedral : 14.872 71.763 1365 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 2.72 % Allowed : 17.97 % Favored : 79.31 % 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: -1.06 (0.27), residues: 933 helix: 0.76 (0.30), residues: 322 sheet: -1.35 (0.37), residues: 152 loop : -1.55 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.009 0.001 PHE B 130 TYR 0.017 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 112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.914 Fit side-chains REVERT: A 83 ARG cc_start: 0.5233 (mpt180) cc_final: 0.4751 (mmp80) REVERT: A 310 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7391 (mp) REVERT: A 480 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6398 (pt0) REVERT: B 44 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6785 (mm-30) REVERT: B 287 LYS cc_start: 0.7023 (tttp) cc_final: 0.6104 (mptt) outliers start: 23 outliers final: 18 residues processed: 107 average time/residue: 0.1925 time to fit residues: 29.8514 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 : 0.943 ------------------------------------------------------------------------------- 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 39 THR 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 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 Chi-restraints excluded: chain B residue 403 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 82 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 58 optimal weight: 0.0980 chunk 47 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.203805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.168856 restraints weight = 9426.874| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.61 r_work: 0.3675 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8772 Z= 0.245 Angle : 0.612 12.809 12063 Z= 0.308 Chirality : 0.043 0.360 1312 Planarity : 0.005 0.058 1396 Dihedral : 14.773 71.558 1365 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.82 % Favored : 95.07 % Rotamer: Outliers : 2.48 % Allowed : 18.56 % Favored : 78.96 % 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: -1.04 (0.27), residues: 933 helix: 0.73 (0.30), residues: 322 sheet: -1.16 (0.37), residues: 152 loop : -1.57 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.009 0.001 PHE B 130 TYR 0.017 0.002 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 108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.900 Fit side-chains REVERT: A 83 ARG cc_start: 0.5256 (mpt180) cc_final: 0.4625 (mmp80) REVERT: A 310 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7398 (mp) REVERT: A 480 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6399 (pt0) REVERT: A 503 LEU cc_start: 0.8041 (tp) cc_final: 0.7805 (mp) REVERT: B 44 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6741 (mm-30) REVERT: B 287 LYS cc_start: 0.7021 (tttp) cc_final: 0.6099 (mptt) REVERT: B 324 ASP cc_start: 0.5968 (t0) cc_final: 0.5718 (t0) outliers start: 21 outliers final: 17 residues processed: 103 average time/residue: 0.1790 time to fit residues: 26.7202 Evaluate side-chains 104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 403 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** B 147 ASN ** 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 = 0.4238 r_free = 0.4238 target = 0.206823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.171579 restraints weight = 9484.701| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.66 r_work: 0.3662 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2108 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= 0.172 Angle : 0.556 12.040 12063 Z= 0.278 Chirality : 0.042 0.364 1312 Planarity : 0.004 0.058 1396 Dihedral : 14.485 70.200 1365 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.68 % Favored : 97.21 % Rotamer: Outliers : 1.30 % Allowed : 19.74 % Favored : 78.96 % 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: -0.68 (0.27), residues: 933 helix: 1.08 (0.31), residues: 322 sheet: -0.93 (0.37), residues: 153 loop : -1.40 (0.28), residues: 458 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 0.007 0.001 PHE A 171 TYR 0.018 0.001 TYR A 183 ARG 0.001 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3631.99 seconds wall clock time: 65 minutes 32.07 seconds (3932.07 seconds total)