Starting phenix.real_space_refine on Tue Jan 14 01:06:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kep_37163/01_2025/8kep_37163.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kep_37163/01_2025/8kep_37163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kep_37163/01_2025/8kep_37163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kep_37163/01_2025/8kep_37163.map" model { file = "/net/cci-nas-00/data/ceres_data/8kep_37163/01_2025/8kep_37163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kep_37163/01_2025/8kep_37163.cif" } resolution = 2.93 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= 0.012 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3060 2.51 5 N 825 2.21 5 O 928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4834 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1615 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "L" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1645 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "A" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1574 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 12, 'TRANS': 183} Time building chain proxies: 4.22, per 1000 atoms: 0.87 Number of scatterers: 4834 At special positions: 0 Unit cell: (74.97, 72.59, 138.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 928 8.00 N 825 7.00 C 3060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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: 1.10 Conformation dependent library (CDL) restraints added in 604.2 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1154 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 13 sheets defined 4.3% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.809A pdb=" N ALA A 372 " --> pdb=" O TYR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.565A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.534A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR H 80 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.890A pdb=" N TRP H 50 " --> pdb=" O ASP H 59 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 128 through 132 removed outlier: 3.506A pdb=" N SER H 128 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS H 151 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU H 132 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER H 188 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 189 " --> pdb=" O HIS H 172 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS H 172 " --> pdb=" O VAL H 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 158 through 162 removed outlier: 3.612A pdb=" N THR H 159 " --> pdb=" O ASN H 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 177 through 178 removed outlier: 3.737A pdb=" N VAL H 177 " --> pdb=" O SER H 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.628A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.678A pdb=" N GLU L 106 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR L 103 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 20 through 22 removed outlier: 3.871A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.720A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN L 161 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 154 through 155 removed outlier: 3.875A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR L 198 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN L 148 " --> pdb=" O GLU L 196 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.811A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.747A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 108 hydrogen bonds defined for protein. 276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1552 1.34 - 1.46: 1239 1.46 - 1.58: 2144 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 4959 Sorted by residual: bond pdb=" C SER L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 1.335 1.354 -0.019 8.70e-03 1.32e+04 4.65e+00 bond pdb=" C LYS H 209 " pdb=" N PRO H 210 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+00 bond pdb=" C TYR A 489 " pdb=" N PHE A 490 " ideal model delta sigma weight residual 1.332 1.353 -0.022 1.92e-02 2.71e+03 1.28e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.15e+00 bond pdb=" C THR L 179 " pdb=" N LEU L 180 " ideal model delta sigma weight residual 1.331 1.342 -0.012 1.29e-02 6.01e+03 8.63e-01 ... (remaining 4954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 6332 1.15 - 2.30: 313 2.30 - 3.46: 82 3.46 - 4.61: 14 4.61 - 5.76: 10 Bond angle restraints: 6751 Sorted by residual: angle pdb=" N TRP H 47 " pdb=" CA TRP H 47 " pdb=" C TRP H 47 " ideal model delta sigma weight residual 108.45 113.85 -5.40 1.26e+00 6.30e-01 1.84e+01 angle pdb=" N ILE A 418 " pdb=" CA ILE A 418 " pdb=" C ILE A 418 " ideal model delta sigma weight residual 112.29 108.26 4.03 9.40e-01 1.13e+00 1.84e+01 angle pdb=" N ASP H 66 " pdb=" CA ASP H 66 " pdb=" C ASP H 66 " ideal model delta sigma weight residual 114.56 109.22 5.34 1.27e+00 6.20e-01 1.77e+01 angle pdb=" N GLU L 82 " pdb=" CA GLU L 82 " pdb=" C GLU L 82 " ideal model delta sigma weight residual 114.09 108.85 5.24 1.55e+00 4.16e-01 1.14e+01 angle pdb=" N SER H 122 " pdb=" CA SER H 122 " pdb=" C SER H 122 " ideal model delta sigma weight residual 107.73 111.58 -3.85 1.34e+00 5.57e-01 8.27e+00 ... (remaining 6746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 2830 17.00 - 33.99: 100 33.99 - 50.99: 17 50.99 - 67.98: 5 67.98 - 84.98: 3 Dihedral angle restraints: 2955 sinusoidal: 1149 harmonic: 1806 Sorted by residual: dihedral pdb=" CA GLU L 80 " pdb=" C GLU L 80 " pdb=" N PRO L 81 " pdb=" CA PRO L 81 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLU H 156 " pdb=" C GLU H 156 " pdb=" N PRO H 157 " pdb=" CA PRO H 157 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" SG CYS H 101 " pdb=" CB CYS H 106 " pdb=" SG CYS H 106 " pdb=" CA CYS H 106 " ideal model delta sinusoidal sigma weight residual -73.00 0.62 -73.62 1 2.00e+01 2.50e-03 1.72e+01 ... (remaining 2952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 431 0.026 - 0.051: 176 0.051 - 0.077: 60 0.077 - 0.102: 54 0.102 - 0.128: 20 Chirality restraints: 741 Sorted by residual: chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL H 129 " pdb=" N VAL H 129 " pdb=" C VAL H 129 " pdb=" CB VAL H 129 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 738 not shown) Planarity restraints: 873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO H 14 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 373 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO H 157 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " 0.018 5.00e-02 4.00e+02 ... (remaining 870 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1606 2.84 - 3.36: 3821 3.36 - 3.87: 7271 3.87 - 4.39: 7869 4.39 - 4.90: 14182 Nonbonded interactions: 34749 Sorted by model distance: nonbonded pdb=" OE1 GLU L 196 " pdb=" OG1 THR L 207 " model vdw 2.328 3.040 nonbonded pdb=" NH1 ARG H 12 " pdb=" O SER H 17 " model vdw 2.337 3.120 nonbonded pdb=" OE2 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.373 3.120 nonbonded pdb=" NZ LYS H 19 " pdb=" OE2 GLU H 82 " model vdw 2.425 3.120 nonbonded pdb=" O PRO H 193 " pdb=" OG SER H 196 " model vdw 2.430 3.040 ... (remaining 34744 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: 2.570 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.870 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 : 0.002 0.038 4959 Z= 0.148 Angle : 0.638 5.760 6751 Z= 0.393 Chirality : 0.041 0.128 741 Planarity : 0.004 0.047 873 Dihedral : 8.962 84.975 1774 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 2.78 % Allowed : 6.68 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.30), residues: 616 helix: -4.63 (0.37), residues: 40 sheet: -1.63 (0.32), residues: 235 loop : -3.62 (0.28), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.001 0.000 HIS H 100 PHE 0.005 0.001 PHE L 140 TYR 0.007 0.001 TYR L 92 ARG 0.002 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.524 Fit side-chains REVERT: H 4 LEU cc_start: 0.7747 (mp) cc_final: 0.7456 (mp) REVERT: H 55 SER cc_start: 0.7961 (t) cc_final: 0.7701 (t) REVERT: H 117 THR cc_start: 0.7706 (m) cc_final: 0.7447 (p) REVERT: L 68 SER cc_start: 0.8073 (p) cc_final: 0.7861 (m) REVERT: L 90 GLN cc_start: 0.8353 (tt0) cc_final: 0.8089 (tt0) REVERT: L 127 LYS cc_start: 0.8929 (mttt) cc_final: 0.8667 (mttt) REVERT: L 133 VAL cc_start: 0.8302 (t) cc_final: 0.8017 (m) REVERT: L 209 SER cc_start: 0.7999 (p) cc_final: 0.7779 (t) REVERT: A 334 ASN cc_start: 0.6235 (p0) cc_final: 0.5833 (t160) outliers start: 15 outliers final: 1 residues processed: 140 average time/residue: 0.9321 time to fit residues: 136.9050 Evaluate side-chains 101 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.0170 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.0040 chunk 55 optimal weight: 0.9980 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN H 100 HIS H 105 ASN H 107 HIS H 179 GLN L 6 GLN L 39 GLN L 90 GLN L 101 GLN A 414 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.148862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.129584 restraints weight = 7662.538| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.65 r_work: 0.3673 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4959 Z= 0.245 Angle : 0.684 12.222 6751 Z= 0.341 Chirality : 0.046 0.147 741 Planarity : 0.005 0.047 873 Dihedral : 4.422 26.277 684 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 4.64 % Allowed : 15.03 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.31), residues: 616 helix: -3.99 (0.58), residues: 34 sheet: -0.67 (0.35), residues: 217 loop : -3.33 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 436 HIS 0.003 0.001 HIS H 172 PHE 0.016 0.002 PHE L 210 TYR 0.014 0.002 TYR L 50 ARG 0.006 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.526 Fit side-chains REVERT: H 4 LEU cc_start: 0.8038 (mp) cc_final: 0.7728 (mp) REVERT: H 55 SER cc_start: 0.8166 (t) cc_final: 0.7933 (t) REVERT: H 58 THR cc_start: 0.8258 (p) cc_final: 0.7966 (p) REVERT: L 90 GLN cc_start: 0.8474 (tt0) cc_final: 0.8185 (tt0) REVERT: L 108 LYS cc_start: 0.8361 (ttpp) cc_final: 0.8047 (mtpp) REVERT: L 109 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7351 (ttp80) REVERT: L 127 LYS cc_start: 0.8984 (mttt) cc_final: 0.8628 (mttt) REVERT: L 133 VAL cc_start: 0.8555 (t) cc_final: 0.8278 (m) REVERT: L 143 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7422 (tpt-90) REVERT: L 209 SER cc_start: 0.7969 (p) cc_final: 0.7607 (t) REVERT: A 334 ASN cc_start: 0.6609 (p0) cc_final: 0.6004 (t160) REVERT: A 386 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6605 (pttt) outliers start: 25 outliers final: 9 residues processed: 119 average time/residue: 0.8842 time to fit residues: 110.8280 Evaluate side-chains 109 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 57 optimal weight: 0.4980 chunk 47 optimal weight: 0.0000 chunk 53 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.148125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.128556 restraints weight = 7601.584| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.67 r_work: 0.3652 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4959 Z= 0.262 Angle : 0.694 10.639 6751 Z= 0.349 Chirality : 0.046 0.165 741 Planarity : 0.005 0.049 873 Dihedral : 4.749 25.947 684 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 5.01 % Allowed : 17.81 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.32), residues: 616 helix: -3.57 (0.69), residues: 34 sheet: -0.28 (0.36), residues: 219 loop : -3.23 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS H 172 PHE 0.016 0.002 PHE A 456 TYR 0.015 0.002 TYR L 174 ARG 0.003 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.528 Fit side-chains REVERT: H 58 THR cc_start: 0.8418 (p) cc_final: 0.8145 (p) REVERT: L 6 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: L 90 GLN cc_start: 0.8378 (tt0) cc_final: 0.8133 (tt0) REVERT: L 127 LYS cc_start: 0.9013 (mttt) cc_final: 0.8638 (mttt) REVERT: L 175 SER cc_start: 0.8347 (t) cc_final: 0.7845 (p) REVERT: L 209 SER cc_start: 0.7885 (p) cc_final: 0.7530 (t) REVERT: A 358 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7682 (mp) REVERT: A 386 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6601 (pttt) outliers start: 27 outliers final: 11 residues processed: 114 average time/residue: 0.9773 time to fit residues: 116.8038 Evaluate side-chains 111 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 16 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.146340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.126912 restraints weight = 7698.707| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.68 r_work: 0.3639 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4959 Z= 0.265 Angle : 0.720 10.564 6751 Z= 0.358 Chirality : 0.047 0.189 741 Planarity : 0.005 0.048 873 Dihedral : 4.971 25.809 684 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 5.01 % Allowed : 18.37 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.32), residues: 616 helix: -3.41 (0.73), residues: 34 sheet: -0.07 (0.36), residues: 219 loop : -3.08 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 149 HIS 0.002 0.001 HIS A 519 PHE 0.018 0.002 PHE A 456 TYR 0.017 0.002 TYR L 174 ARG 0.008 0.000 ARG L 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.557 Fit side-chains REVERT: H 58 THR cc_start: 0.8495 (p) cc_final: 0.8241 (p) REVERT: H 74 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8287 (mtp) REVERT: L 10 THR cc_start: 0.8419 (p) cc_final: 0.8050 (m) REVERT: L 105 VAL cc_start: 0.8265 (t) cc_final: 0.8038 (m) REVERT: L 127 LYS cc_start: 0.9012 (mttt) cc_final: 0.8649 (mttt) REVERT: L 147 VAL cc_start: 0.9149 (m) cc_final: 0.8919 (p) REVERT: L 175 SER cc_start: 0.8311 (t) cc_final: 0.7835 (p) REVERT: L 209 SER cc_start: 0.7870 (p) cc_final: 0.7524 (t) REVERT: A 386 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6669 (pttt) outliers start: 27 outliers final: 18 residues processed: 120 average time/residue: 0.8583 time to fit residues: 108.7754 Evaluate side-chains 121 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.0000 chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 47 optimal weight: 0.0670 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 overall best weight: 0.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.149463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129967 restraints weight = 7693.358| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.65 r_work: 0.3679 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4959 Z= 0.168 Angle : 0.672 11.437 6751 Z= 0.321 Chirality : 0.045 0.156 741 Planarity : 0.004 0.046 873 Dihedral : 4.594 24.674 684 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 4.45 % Allowed : 20.59 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.33), residues: 616 helix: -3.32 (0.75), residues: 34 sheet: 0.10 (0.36), residues: 219 loop : -2.92 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.000 HIS A 519 PHE 0.014 0.001 PHE L 210 TYR 0.012 0.001 TYR A 501 ARG 0.005 0.000 ARG L 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.497 Fit side-chains REVERT: H 58 THR cc_start: 0.8406 (p) cc_final: 0.8146 (p) REVERT: H 81 MET cc_start: 0.8503 (ttp) cc_final: 0.8218 (ttt) REVERT: H 132 LEU cc_start: 0.7131 (tm) cc_final: 0.6882 (tt) REVERT: L 6 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: L 10 THR cc_start: 0.8431 (p) cc_final: 0.8046 (m) REVERT: L 20 THR cc_start: 0.8867 (p) cc_final: 0.8536 (p) REVERT: L 90 GLN cc_start: 0.8346 (tt0) cc_final: 0.8109 (tt0) REVERT: L 105 VAL cc_start: 0.8169 (t) cc_final: 0.7913 (m) REVERT: L 108 LYS cc_start: 0.8445 (ttpp) cc_final: 0.8136 (mtpp) REVERT: L 127 LYS cc_start: 0.9014 (mttt) cc_final: 0.8648 (mttt) REVERT: L 143 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7014 (tmt90) REVERT: L 147 VAL cc_start: 0.9193 (m) cc_final: 0.8961 (p) REVERT: L 175 SER cc_start: 0.8299 (t) cc_final: 0.7846 (p) REVERT: L 209 SER cc_start: 0.7783 (p) cc_final: 0.7488 (t) REVERT: A 358 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7592 (mp) outliers start: 24 outliers final: 13 residues processed: 123 average time/residue: 0.8510 time to fit residues: 110.4766 Evaluate side-chains 117 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.7887 > 50: distance: 12 - 14: 17.226 distance: 14 - 15: 20.240 distance: 15 - 16: 20.845 distance: 15 - 18: 23.190 distance: 16 - 17: 23.916 distance: 16 - 21: 20.557 distance: 18 - 19: 25.122 distance: 18 - 20: 29.090 distance: 21 - 22: 37.778 distance: 22 - 23: 9.500 distance: 22 - 25: 61.789 distance: 23 - 24: 12.656 distance: 23 - 27: 37.133 distance: 25 - 26: 41.950 distance: 27 - 28: 8.077 distance: 27 - 33: 16.462 distance: 28 - 29: 30.168 distance: 28 - 31: 43.557 distance: 29 - 30: 30.505 distance: 29 - 34: 12.020 distance: 31 - 32: 13.941 distance: 32 - 33: 24.779 distance: 34 - 35: 9.661 distance: 35 - 36: 16.800 distance: 35 - 38: 15.928 distance: 36 - 37: 24.240 distance: 36 - 41: 3.924 distance: 38 - 39: 7.718 distance: 38 - 40: 13.826 distance: 41 - 42: 8.745 distance: 42 - 43: 17.239 distance: 42 - 45: 19.327 distance: 43 - 44: 19.157 distance: 43 - 50: 23.397 distance: 45 - 46: 11.299 distance: 47 - 48: 5.085 distance: 50 - 51: 27.669 distance: 51 - 52: 20.796 distance: 51 - 54: 45.464 distance: 52 - 53: 29.142 distance: 52 - 58: 10.475 distance: 54 - 55: 13.873 distance: 55 - 56: 19.591 distance: 55 - 57: 31.251 distance: 58 - 59: 18.541 distance: 59 - 60: 20.531 distance: 59 - 62: 17.673 distance: 60 - 61: 44.626 distance: 60 - 66: 17.467 distance: 62 - 63: 27.288 distance: 63 - 64: 19.357 distance: 63 - 65: 26.962 distance: 66 - 67: 11.589 distance: 67 - 68: 28.571 distance: 67 - 70: 18.183 distance: 68 - 69: 44.479 distance: 68 - 74: 29.643 distance: 70 - 71: 3.577 distance: 71 - 72: 14.815 distance: 71 - 73: 14.870 distance: 74 - 75: 8.556 distance: 75 - 76: 9.845 distance: 75 - 78: 16.064 distance: 76 - 77: 32.414 distance: 76 - 82: 13.703 distance: 78 - 79: 19.467 distance: 79 - 80: 4.266 distance: 79 - 81: 8.921 distance: 82 - 83: 17.034 distance: 83 - 84: 10.189 distance: 83 - 86: 7.387 distance: 84 - 85: 20.291 distance: 84 - 88: 9.724 distance: 86 - 87: 15.537 distance: 87 - 119: 7.057