Starting phenix.real_space_refine on Tue Mar 3 19:40:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2e_14463/03_2026/7z2e_14463.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2e_14463/03_2026/7z2e_14463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2e_14463/03_2026/7z2e_14463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2e_14463/03_2026/7z2e_14463.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2e_14463/03_2026/7z2e_14463.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2e_14463/03_2026/7z2e_14463.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 12 5.16 5 C 5380 2.51 5 N 1418 2.21 5 O 1634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8479 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4331 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 496} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3399 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 381} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 721 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'T27': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.01, per 1000 atoms: 0.24 Number of scatterers: 8479 At special positions: 0 Unit cell: (97.97, 112.52, 101.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 35 15.00 O 1634 8.00 N 1418 7.00 C 5380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 291.2 milliseconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 37.8% alpha, 13.3% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 77 through 82 removed outlier: 4.007A pdb=" N LYS A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.585A pdb=" N TYR A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.791A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 removed outlier: 4.006A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.704A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.569A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.602A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.535A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.577A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 removed outlier: 4.239A pdb=" N ALA A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.854A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 removed outlier: 3.574A pdb=" N LYS B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.804A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.639A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.170A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 213 removed outlier: 3.580A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.627A pdb=" N LYS B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 296 through 311 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 removed outlier: 4.041A pdb=" N SER A 48 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 145 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.511A pdb=" N PHE A 227 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 354 removed outlier: 7.478A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 464 through 468 removed outlier: 3.887A pdb=" N VAL A 467 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 455 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AA9, first strand: chain 'B' and resid 350 through 355 removed outlier: 3.925A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.93 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.180 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.840 ------------------------------------------------------------------------------- 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= 0.252 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.28), residues: 933 helix: 1.33 (0.31), residues: 311 sheet: -0.70 (0.40), residues: 161 loop : -1.34 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.014 0.001 TYR A 501 PHE 0.017 0.001 PHE B 87 TRP 0.014 0.001 TRP B 266 HIS 0.003 0.000 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 8772) covalent geometry : angle 0.76266 (12063) hydrogen bonds : bond 0.13490 ( 333) hydrogen bonds : angle 6.54242 ( 897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.306 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: 0.0916 time to fit residues: 14.9398 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN A 547 GLN B 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.204821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.169847 restraints weight = 9429.036| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.83 r_work: 0.3621 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8772 Z= 0.133 Angle : 0.551 6.189 12063 Z= 0.284 Chirality : 0.041 0.139 1312 Planarity : 0.005 0.080 1396 Dihedral : 15.364 67.860 1365 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 1.18 % Allowed : 7.33 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.28), residues: 933 helix: 1.44 (0.31), residues: 311 sheet: -0.53 (0.40), residues: 154 loop : -1.27 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 356 TYR 0.020 0.001 TYR A 501 PHE 0.020 0.001 PHE B 87 TRP 0.019 0.001 TRP A 406 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8772) covalent geometry : angle 0.55063 (12063) hydrogen bonds : bond 0.03784 ( 333) hydrogen bonds : angle 4.26480 ( 897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.296 Fit side-chains REVERT: A 83 ARG cc_start: 0.5156 (mpt180) cc_final: 0.4510 (mmp80) REVERT: A 256 ASP cc_start: 0.6987 (m-30) cc_final: 0.6784 (m-30) REVERT: B 44 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6319 (mt-10) outliers start: 10 outliers final: 7 residues processed: 106 average time/residue: 0.0870 time to fit residues: 12.9804 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 : 0.248 ------------------------------------------------------------------------------- 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 472 THR Chi-restraints excluded: chain A residue 531 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 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 = 0.203973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.168676 restraints weight = 9391.880| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.79 r_work: 0.3623 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8772 Z= 0.178 Angle : 0.596 6.297 12063 Z= 0.306 Chirality : 0.043 0.145 1312 Planarity : 0.005 0.071 1396 Dihedral : 15.283 68.994 1365 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 1.65 % Allowed : 12.17 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.27), residues: 933 helix: 1.09 (0.30), residues: 318 sheet: -0.97 (0.39), residues: 152 loop : -1.38 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.016 0.002 TYR A 501 PHE 0.016 0.002 PHE A 171 TRP 0.024 0.002 TRP A 406 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8772) covalent geometry : angle 0.59632 (12063) hydrogen bonds : bond 0.04125 ( 333) hydrogen bonds : angle 4.44052 ( 897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.199 Fit side-chains REVERT: A 83 ARG cc_start: 0.5119 (mpt180) cc_final: 0.4717 (mmp80) REVERT: B 342 TYR cc_start: 0.7994 (p90) cc_final: 0.7721 (p90) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 0.0816 time to fit residues: 12.2985 Evaluate side-chains 95 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 83 optimal weight: 30.0000 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 88 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 0.0020 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- 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 = 0.203711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.168050 restraints weight = 9547.640| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.76 r_work: 0.3587 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8772 Z= 0.183 Angle : 0.603 7.896 12063 Z= 0.310 Chirality : 0.043 0.166 1312 Planarity : 0.005 0.067 1396 Dihedral : 15.235 69.551 1365 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 2.84 % Allowed : 13.00 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.27), residues: 933 helix: 0.90 (0.30), residues: 318 sheet: -1.16 (0.38), residues: 153 loop : -1.53 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.015 0.002 TYR B 342 PHE 0.014 0.002 PHE A 171 TRP 0.028 0.002 TRP A 406 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8772) covalent geometry : angle 0.60348 (12063) hydrogen bonds : bond 0.04052 ( 333) hydrogen bonds : angle 4.51687 ( 897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.296 Fit side-chains REVERT: A 83 ARG cc_start: 0.5040 (mpt180) cc_final: 0.4620 (mmp80) REVERT: A 185 ASP cc_start: 0.4855 (OUTLIER) cc_final: 0.4528 (t0) REVERT: A 256 ASP cc_start: 0.6889 (m-30) cc_final: 0.6671 (m-30) REVERT: A 503 LEU cc_start: 0.8070 (tp) cc_final: 0.7730 (mp) REVERT: B 44 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6874 (mm-30) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.0764 time to fit residues: 12.5424 Evaluate side-chains 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 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 525 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 397 THR 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 71 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 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 = 0.204843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.169130 restraints weight = 9481.818| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.69 r_work: 0.3647 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8772 Z= 0.140 Angle : 0.559 6.308 12063 Z= 0.288 Chirality : 0.041 0.150 1312 Planarity : 0.004 0.063 1396 Dihedral : 15.024 69.840 1365 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 2.36 % Allowed : 14.78 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.27), residues: 933 helix: 1.17 (0.31), residues: 316 sheet: -1.03 (0.37), residues: 156 loop : -1.43 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.014 0.001 TYR A 144 PHE 0.012 0.001 PHE A 171 TRP 0.029 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8772) covalent geometry : angle 0.55924 (12063) hydrogen bonds : bond 0.03560 ( 333) hydrogen bonds : angle 4.38340 ( 897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.200 Fit side-chains REVERT: A 83 ARG cc_start: 0.5113 (mpt180) cc_final: 0.4692 (mmp80) REVERT: A 185 ASP cc_start: 0.4704 (OUTLIER) cc_final: 0.4342 (t0) REVERT: A 310 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7431 (mp) REVERT: A 480 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6144 (pt0) REVERT: B 44 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6838 (mm-30) outliers start: 20 outliers final: 9 residues processed: 104 average time/residue: 0.0736 time to fit residues: 11.0184 Evaluate side-chains 94 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 B 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.204539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170613 restraints weight = 9428.156| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.54 r_work: 0.3674 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8772 Z= 0.223 Angle : 0.659 8.596 12063 Z= 0.338 Chirality : 0.045 0.262 1312 Planarity : 0.005 0.060 1396 Dihedral : 15.231 72.686 1365 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.14 % Favored : 94.75 % Rotamer: Outliers : 2.72 % Allowed : 16.78 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.27), residues: 933 helix: 0.62 (0.30), residues: 324 sheet: -1.18 (0.38), residues: 153 loop : -1.64 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.017 0.002 TYR A 457 PHE 0.020 0.002 PHE A 171 TRP 0.031 0.002 TRP A 406 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 8772) covalent geometry : angle 0.65881 (12063) hydrogen bonds : bond 0.04464 ( 333) hydrogen bonds : angle 4.73827 ( 897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.313 Fit side-chains REVERT: A 83 ARG cc_start: 0.5085 (mpt180) cc_final: 0.4670 (mmp80) REVERT: A 310 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7504 (mp) REVERT: A 480 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6456 (pt0) REVERT: B 287 LYS cc_start: 0.7097 (tttp) cc_final: 0.6103 (mptt) outliers start: 23 outliers final: 16 residues processed: 103 average time/residue: 0.0767 time to fit residues: 11.7765 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.204770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.168743 restraints weight = 9551.582| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.67 r_work: 0.3659 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8772 Z= 0.133 Angle : 0.561 6.776 12063 Z= 0.287 Chirality : 0.042 0.219 1312 Planarity : 0.004 0.057 1396 Dihedral : 14.898 69.745 1365 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.36 % Rotamer: Outliers : 2.60 % Allowed : 17.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.27), residues: 933 helix: 1.01 (0.31), residues: 316 sheet: -1.29 (0.37), residues: 153 loop : -1.54 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.015 0.001 TYR A 144 PHE 0.016 0.001 PHE A 171 TRP 0.034 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8772) covalent geometry : angle 0.56100 (12063) hydrogen bonds : bond 0.03499 ( 333) hydrogen bonds : angle 4.47120 ( 897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.330 Fit side-chains REVERT: A 83 ARG cc_start: 0.5036 (mpt180) cc_final: 0.4603 (mmp80) REVERT: A 310 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7427 (mp) REVERT: A 480 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6346 (pt0) REVERT: B 44 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6201 (mt-10) REVERT: B 287 LYS cc_start: 0.6931 (tttp) cc_final: 0.6015 (mptt) outliers start: 22 outliers final: 15 residues processed: 108 average time/residue: 0.0818 time to fit residues: 12.8266 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 : 0.305 ------------------------------------------------------------------------------- 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 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 370 GLU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.208646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.174904 restraints weight = 9368.182| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.55 r_work: 0.3696 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8772 Z= 0.139 Angle : 0.581 11.989 12063 Z= 0.293 Chirality : 0.043 0.375 1312 Planarity : 0.004 0.056 1396 Dihedral : 14.847 69.903 1365 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 2.13 % Allowed : 18.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.27), residues: 933 helix: 1.03 (0.31), residues: 316 sheet: -1.05 (0.38), residues: 153 loop : -1.54 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.015 0.001 TYR A 457 PHE 0.018 0.001 PHE A 171 TRP 0.038 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8772) covalent geometry : angle 0.58086 (12063) hydrogen bonds : bond 0.03530 ( 333) hydrogen bonds : angle 4.48604 ( 897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.311 Fit side-chains REVERT: A 83 ARG cc_start: 0.5155 (mpt180) cc_final: 0.4647 (mmp80) REVERT: A 310 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7498 (mp) REVERT: A 480 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6423 (pt0) REVERT: B 44 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6305 (mt-10) outliers start: 18 outliers final: 14 residues processed: 100 average time/residue: 0.0774 time to fit residues: 11.3926 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 480 GLN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 542 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 370 GLU Chi-restraints excluded: chain B residue 397 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 90 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 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 = 0.4209 r_free = 0.4209 target = 0.203138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.167325 restraints weight = 9492.097| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.64 r_work: 0.3616 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8772 Z= 0.184 Angle : 0.632 12.978 12063 Z= 0.320 Chirality : 0.044 0.326 1312 Planarity : 0.005 0.055 1396 Dihedral : 14.930 72.464 1365 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.93 % Favored : 94.96 % Rotamer: Outliers : 2.48 % Allowed : 18.32 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.27), residues: 933 helix: 0.74 (0.30), residues: 322 sheet: -1.26 (0.37), residues: 156 loop : -1.55 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.018 0.002 TYR A 457 PHE 0.012 0.002 PHE B 130 TRP 0.035 0.002 TRP A 406 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8772) covalent geometry : angle 0.63243 (12063) hydrogen bonds : bond 0.04002 ( 333) hydrogen bonds : angle 4.68386 ( 897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.338 Fit side-chains REVERT: A 83 ARG cc_start: 0.5022 (mpt180) cc_final: 0.4554 (mmp80) REVERT: A 310 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7386 (mp) REVERT: A 480 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6485 (pt0) REVERT: B 287 LYS cc_start: 0.7024 (tttp) cc_final: 0.6097 (mptt) outliers start: 21 outliers final: 17 residues processed: 100 average time/residue: 0.0740 time to fit residues: 11.0319 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 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 71 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN A 547 GLN B 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.201108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.166895 restraints weight = 9510.599| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.77 r_work: 0.3623 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8772 Z= 0.211 Angle : 0.667 12.286 12063 Z= 0.340 Chirality : 0.045 0.324 1312 Planarity : 0.005 0.057 1396 Dihedral : 14.913 73.984 1365 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.25 % Favored : 94.64 % Rotamer: Outliers : 2.25 % Allowed : 18.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.27), residues: 933 helix: 0.54 (0.30), residues: 322 sheet: -1.35 (0.37), residues: 153 loop : -1.64 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.020 0.002 TYR A 457 PHE 0.013 0.002 PHE B 130 TRP 0.030 0.002 TRP A 406 HIS 0.003 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8772) covalent geometry : angle 0.66654 (12063) hydrogen bonds : bond 0.04353 ( 333) hydrogen bonds : angle 4.84158 ( 897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.296 Fit side-chains REVERT: A 83 ARG cc_start: 0.5060 (mpt180) cc_final: 0.4586 (mmp80) REVERT: A 310 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7438 (mp) REVERT: B 44 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6470 (mt-10) REVERT: B 287 LYS cc_start: 0.7149 (tttp) cc_final: 0.6167 (mptt) outliers start: 19 outliers final: 15 residues processed: 99 average time/residue: 0.0772 time to fit residues: 11.2235 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.205006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.169262 restraints weight = 9319.241| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.65 r_work: 0.3609 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8772 Z= 0.141 Angle : 0.590 11.218 12063 Z= 0.299 Chirality : 0.043 0.326 1312 Planarity : 0.005 0.057 1396 Dihedral : 14.612 70.143 1365 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.86 % Favored : 96.03 % Rotamer: Outliers : 2.01 % Allowed : 18.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.27), residues: 933 helix: 0.92 (0.31), residues: 317 sheet: -1.20 (0.37), residues: 153 loop : -1.50 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.015 0.002 TYR A 183 PHE 0.009 0.001 PHE B 130 TRP 0.034 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8772) covalent geometry : angle 0.58999 (12063) hydrogen bonds : bond 0.03553 ( 333) hydrogen bonds : angle 4.58153 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.46 seconds wall clock time: 30 minutes 30.27 seconds (1830.27 seconds total)