Starting phenix.real_space_refine on Sat May 10 16:15:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u9o_26402/05_2025/7u9o_26402.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u9o_26402/05_2025/7u9o_26402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u9o_26402/05_2025/7u9o_26402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u9o_26402/05_2025/7u9o_26402.map" model { file = "/net/cci-nas-00/data/ceres_data/7u9o_26402/05_2025/7u9o_26402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u9o_26402/05_2025/7u9o_26402.cif" } resolution = 3.4 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= 0.002 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 25 5.16 5 C 4196 2.51 5 N 1088 2.21 5 O 1254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6563 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2078 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 15, 'TRANS': 248} Chain breaks: 2 Chain: "B" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1472 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 9 Chain: "H" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1519 Classifications: {'peptide': 199} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 185} Chain breaks: 4 Chain: "L" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1452 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.06, per 1000 atoms: 0.62 Number of scatterers: 6563 At special positions: 0 Unit cell: (94.284, 105.633, 142.299, 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 25 16.00 O 1254 8.00 N 1088 7.00 C 4196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B1301 " - " ASN B 234 " Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 814.2 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 20 sheets defined 5.3% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.081A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.808A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.046A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.825A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.904A pdb=" N SER L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 379 Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.773A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.737A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.674A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.656A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.525A pdb=" N GLU H 99 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.223A pdb=" N VAL H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 131 through 135 removed outlier: 5.822A pdb=" N GLY H 150 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL H 193 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU H 152 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER H 191 " --> pdb=" O LEU H 152 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LYS H 154 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU H 189 " --> pdb=" O LYS H 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.900A pdb=" N VAL H 209 " --> pdb=" O TRP H 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 162 through 165 removed outlier: 4.332A pdb=" N TYR H 205 " --> pdb=" O LEU H 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.650A pdb=" N TYR L 32 " --> pdb=" O ARG L 91 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.591A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 117 through 119 removed outlier: 3.661A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU L 176 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER L 163 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN L 161 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 146 through 148 175 hydrogen bonds defined for protein. 405 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: 1.78 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2066 1.34 - 1.47: 1784 1.47 - 1.59: 2841 1.59 - 1.72: 0 1.72 - 1.85: 29 Bond restraints: 6720 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.28e+00 bond pdb=" CB ARG A 509 " pdb=" CG ARG A 509 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.93e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" N THR L 98 " pdb=" CA THR L 98 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.17e+00 ... (remaining 6715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 8700 1.94 - 3.88: 368 3.88 - 5.82: 44 5.82 - 7.76: 18 7.76 - 9.69: 3 Bond angle restraints: 9133 Sorted by residual: angle pdb=" N GLN L 27 " pdb=" CA GLN L 27 " pdb=" C GLN L 27 " ideal model delta sigma weight residual 110.80 120.49 -9.69 2.13e+00 2.20e-01 2.07e+01 angle pdb=" N GLY A 566 " pdb=" CA GLY A 566 " pdb=" C GLY A 566 " ideal model delta sigma weight residual 113.18 122.83 -9.65 2.37e+00 1.78e-01 1.66e+01 angle pdb=" C ALA H 214 " pdb=" N THR H 215 " pdb=" CA THR H 215 " ideal model delta sigma weight residual 124.21 128.84 -4.63 1.21e+00 6.83e-01 1.47e+01 angle pdb=" CA TRP L 94 " pdb=" C TRP L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 118.44 124.23 -5.79 1.59e+00 3.96e-01 1.33e+01 angle pdb=" C SER L 26 " pdb=" N GLN L 27 " pdb=" CA GLN L 27 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 ... (remaining 9128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 3788 15.35 - 30.69: 167 30.69 - 46.04: 44 46.04 - 61.39: 6 61.39 - 76.73: 6 Dihedral angle restraints: 4011 sinusoidal: 1615 harmonic: 2396 Sorted by residual: dihedral pdb=" CA TYR L 141 " pdb=" C TYR L 141 " pdb=" N PRO L 142 " pdb=" CA PRO L 142 " ideal model delta harmonic sigma weight residual 180.00 122.54 57.46 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA SER L 26 " pdb=" C SER L 26 " pdb=" N GLN L 27 " pdb=" CA GLN L 27 " ideal model delta harmonic sigma weight residual -180.00 -145.65 -34.35 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLN L 27 " pdb=" C GLN L 27 " pdb=" N SER L 28 " pdb=" CA SER L 28 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 4008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 694 0.053 - 0.105: 241 0.105 - 0.158: 70 0.158 - 0.211: 15 0.211 - 0.263: 3 Chirality restraints: 1023 Sorted by residual: chirality pdb=" CB THR L 98 " pdb=" CA THR L 98 " pdb=" OG1 THR L 98 " pdb=" CG2 THR L 98 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TRP L 94 " pdb=" N TRP L 94 " pdb=" C TRP L 94 " pdb=" CB TRP L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB THR H 106 " pdb=" CA THR H 106 " pdb=" OG1 THR H 106 " pdb=" CG2 THR H 106 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1020 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 141 " 0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO L 142 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO L 142 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 142 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 347 " 0.021 2.00e-02 2.50e+03 2.22e-02 8.61e+00 pdb=" CG PHE A 347 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 347 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 347 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 347 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 347 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 347 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU L 79 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO L 80 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.033 5.00e-02 4.00e+02 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2046 2.84 - 3.36: 4905 3.36 - 3.87: 9794 3.87 - 4.39: 10568 4.39 - 4.90: 19739 Nonbonded interactions: 47052 Sorted by model distance: nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.330 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.330 3.040 nonbonded pdb=" OG SER A 555 " pdb=" OD1 ASP A 586 " model vdw 2.364 3.040 nonbonded pdb=" O ILE L 107 " pdb=" OH TYR L 141 " model vdw 2.390 3.040 nonbonded pdb=" NH1 ARG L 109 " pdb=" O ASP L 171 " model vdw 2.399 3.120 ... (remaining 47047 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: 1.030 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.490 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.007 0.073 6733 Z= 0.301 Angle : 0.932 9.694 9162 Z= 0.509 Chirality : 0.060 0.263 1023 Planarity : 0.009 0.081 1164 Dihedral : 10.076 76.733 2437 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.53 % Favored : 90.34 % Rotamer: Outliers : 0.28 % Allowed : 2.34 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.13 % 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: -4.13 (0.26), residues: 787 helix: -4.44 (0.42), residues: 32 sheet: -2.18 (0.29), residues: 282 loop : -3.10 (0.24), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 114 HIS 0.020 0.004 HIS H 35 PHE 0.050 0.003 PHE A 347 TYR 0.037 0.004 TYR A 495 ARG 0.010 0.001 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 3) link_NAG-ASN : angle 3.67077 ( 9) hydrogen bonds : bond 0.27128 ( 164) hydrogen bonds : angle 10.35878 ( 405) SS BOND : bond 0.00714 ( 10) SS BOND : angle 2.08299 ( 20) covalent geometry : bond 0.00721 ( 6720) covalent geometry : angle 0.92126 ( 9133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 361 CYS cc_start: 0.5699 (p) cc_final: 0.5349 (p) REVERT: A 574 ASP cc_start: 0.8199 (p0) cc_final: 0.7963 (p0) REVERT: A 584 ILE cc_start: 0.8811 (mm) cc_final: 0.8596 (mp) REVERT: A 586 ASP cc_start: 0.7872 (m-30) cc_final: 0.7643 (t0) REVERT: B 41 LYS cc_start: 0.8265 (mtpt) cc_final: 0.6500 (tptt) REVERT: B 134 GLN cc_start: 0.6283 (tp40) cc_final: 0.5897 (pm20) REVERT: B 202 LYS cc_start: 0.8288 (mttp) cc_final: 0.7828 (mttm) REVERT: B 278 LYS cc_start: 0.8149 (tttt) cc_final: 0.6933 (mttt) REVERT: H 220 ARG cc_start: 0.7815 (tpt170) cc_final: 0.7604 (tpp-160) outliers start: 2 outliers final: 1 residues processed: 175 average time/residue: 0.2242 time to fit residues: 49.9767 Evaluate side-chains 114 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.0030 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN B 188 ASN B 282 ASN H 208 ASN L 6 GLN L 90 GLN L 167 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106019 restraints weight = 8088.592| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.49 r_work: 0.3065 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6733 Z= 0.117 Angle : 0.651 13.877 9162 Z= 0.328 Chirality : 0.047 0.226 1023 Planarity : 0.006 0.069 1164 Dihedral : 7.681 65.029 951 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.20 % Allowed : 5.51 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -3.27 (0.27), residues: 787 helix: -4.01 (0.43), residues: 26 sheet: -1.19 (0.33), residues: 262 loop : -2.78 (0.24), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE B 220 TYR 0.015 0.002 TYR A 495 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00642 ( 3) link_NAG-ASN : angle 2.36871 ( 9) hydrogen bonds : bond 0.03509 ( 164) hydrogen bonds : angle 6.85814 ( 405) SS BOND : bond 0.00295 ( 10) SS BOND : angle 0.89420 ( 20) covalent geometry : bond 0.00264 ( 6720) covalent geometry : angle 0.64617 ( 9133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.714 Fit side-chains REVERT: A 361 CYS cc_start: 0.6627 (p) cc_final: 0.6188 (p) REVERT: A 525 CYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6710 (m) REVERT: B 41 LYS cc_start: 0.8247 (mtpt) cc_final: 0.6402 (tptt) REVERT: B 134 GLN cc_start: 0.6128 (tp40) cc_final: 0.5660 (pm20) REVERT: B 237 ARG cc_start: 0.7754 (mtm180) cc_final: 0.6480 (ttm-80) REVERT: B 278 LYS cc_start: 0.8314 (tttt) cc_final: 0.8111 (tttt) REVERT: H 149 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8067 (pp) REVERT: H 220 ARG cc_start: 0.7904 (tpt170) cc_final: 0.7590 (tpp-160) REVERT: L 11 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7979 (tt) REVERT: L 177 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8612 (m) outliers start: 16 outliers final: 8 residues processed: 133 average time/residue: 0.1994 time to fit residues: 34.4841 Evaluate side-chains 121 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 186 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN L 125 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103136 restraints weight = 8226.202| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.50 r_work: 0.3013 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6733 Z= 0.185 Angle : 0.676 10.148 9162 Z= 0.343 Chirality : 0.048 0.201 1023 Planarity : 0.006 0.096 1164 Dihedral : 7.617 68.812 951 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.89 % Allowed : 7.30 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.91 (0.28), residues: 787 helix: -3.26 (0.62), residues: 26 sheet: -1.05 (0.33), residues: 258 loop : -2.48 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 114 HIS 0.008 0.002 HIS H 35 PHE 0.017 0.002 PHE A 347 TYR 0.023 0.002 TYR A 495 ARG 0.004 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00775 ( 3) link_NAG-ASN : angle 3.52692 ( 9) hydrogen bonds : bond 0.03701 ( 164) hydrogen bonds : angle 6.13351 ( 405) SS BOND : bond 0.00423 ( 10) SS BOND : angle 1.15639 ( 20) covalent geometry : bond 0.00447 ( 6720) covalent geometry : angle 0.66605 ( 9133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.7074 (pt) REVERT: A 361 CYS cc_start: 0.6763 (p) cc_final: 0.6340 (p) REVERT: A 586 ASP cc_start: 0.8139 (m-30) cc_final: 0.7782 (m-30) REVERT: B 41 LYS cc_start: 0.8272 (mtpt) cc_final: 0.6395 (tptt) REVERT: B 134 GLN cc_start: 0.6289 (tp40) cc_final: 0.5785 (pm20) REVERT: H 116 GLN cc_start: 0.8795 (pm20) cc_final: 0.8212 (pm20) REVERT: H 186 LEU cc_start: 0.8555 (mp) cc_final: 0.8259 (mt) REVERT: L 11 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7988 (tt) REVERT: L 109 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.5952 (ppp80) outliers start: 21 outliers final: 12 residues processed: 128 average time/residue: 0.2058 time to fit residues: 34.3126 Evaluate side-chains 118 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 186 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.146486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103440 restraints weight = 8307.187| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.51 r_work: 0.3002 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6733 Z= 0.151 Angle : 0.632 11.584 9162 Z= 0.318 Chirality : 0.046 0.204 1023 Planarity : 0.006 0.093 1164 Dihedral : 7.398 69.462 950 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.75 % Allowed : 9.37 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.55 (0.28), residues: 787 helix: -2.73 (0.75), residues: 26 sheet: -0.72 (0.33), residues: 259 loop : -2.29 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.006 0.001 HIS H 35 PHE 0.020 0.002 PHE A 541 TYR 0.023 0.002 TYR L 141 ARG 0.003 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 3) link_NAG-ASN : angle 3.15734 ( 9) hydrogen bonds : bond 0.03211 ( 164) hydrogen bonds : angle 5.73868 ( 405) SS BOND : bond 0.00303 ( 10) SS BOND : angle 0.84716 ( 20) covalent geometry : bond 0.00361 ( 6720) covalent geometry : angle 0.62428 ( 9133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8144 (m-30) cc_final: 0.7768 (m-30) REVERT: B 41 LYS cc_start: 0.8211 (mtpt) cc_final: 0.6326 (tptt) REVERT: B 134 GLN cc_start: 0.6410 (tp40) cc_final: 0.5867 (pm20) REVERT: B 202 LYS cc_start: 0.8628 (mttp) cc_final: 0.7990 (mtpm) REVERT: H 186 LEU cc_start: 0.8526 (mp) cc_final: 0.8223 (mt) REVERT: L 11 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7910 (tt) REVERT: L 168 ASP cc_start: 0.7579 (t0) cc_final: 0.7180 (t0) outliers start: 20 outliers final: 15 residues processed: 129 average time/residue: 0.1989 time to fit residues: 33.7221 Evaluate side-chains 123 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 186 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 3 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104490 restraints weight = 8284.662| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.52 r_work: 0.3130 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6733 Z= 0.110 Angle : 0.589 11.142 9162 Z= 0.294 Chirality : 0.045 0.195 1023 Planarity : 0.005 0.085 1164 Dihedral : 6.956 67.540 950 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.03 % Allowed : 10.19 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.22 (0.29), residues: 787 helix: -2.55 (0.81), residues: 26 sheet: -0.47 (0.32), residues: 270 loop : -2.11 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE B 238 TYR 0.018 0.001 TYR L 141 ARG 0.002 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 3) link_NAG-ASN : angle 3.01254 ( 9) hydrogen bonds : bond 0.02841 ( 164) hydrogen bonds : angle 5.46754 ( 405) SS BOND : bond 0.00324 ( 10) SS BOND : angle 0.67662 ( 20) covalent geometry : bond 0.00254 ( 6720) covalent geometry : angle 0.58162 ( 9133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 CYS cc_start: 0.6759 (p) cc_final: 0.6305 (p) REVERT: A 386 LYS cc_start: 0.8148 (tppt) cc_final: 0.7121 (tttt) REVERT: A 586 ASP cc_start: 0.8157 (m-30) cc_final: 0.7819 (m-30) REVERT: B 41 LYS cc_start: 0.8169 (mtpt) cc_final: 0.6289 (tptt) REVERT: B 101 ILE cc_start: 0.8579 (mm) cc_final: 0.8343 (mm) REVERT: B 134 GLN cc_start: 0.6408 (tp40) cc_final: 0.5881 (pm20) REVERT: B 237 ARG cc_start: 0.7800 (mtm180) cc_final: 0.6622 (mtm-85) REVERT: H 159 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7722 (mt-10) REVERT: H 186 LEU cc_start: 0.8553 (mp) cc_final: 0.8265 (mt) REVERT: L 168 ASP cc_start: 0.7547 (t0) cc_final: 0.7302 (t0) outliers start: 22 outliers final: 19 residues processed: 129 average time/residue: 0.1870 time to fit residues: 31.6148 Evaluate side-chains 127 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 0.0170 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107294 restraints weight = 8170.435| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.51 r_work: 0.3068 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6733 Z= 0.088 Angle : 0.550 10.629 9162 Z= 0.271 Chirality : 0.044 0.157 1023 Planarity : 0.005 0.086 1164 Dihedral : 6.174 57.529 950 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.62 % Allowed : 10.88 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.30), residues: 787 helix: -2.44 (0.82), residues: 26 sheet: -0.19 (0.33), residues: 277 loop : -1.91 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 94 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE L 99 TYR 0.018 0.001 TYR L 141 ARG 0.003 0.000 ARG L 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 3) link_NAG-ASN : angle 3.14111 ( 9) hydrogen bonds : bond 0.02514 ( 164) hydrogen bonds : angle 5.11436 ( 405) SS BOND : bond 0.00148 ( 10) SS BOND : angle 0.54486 ( 20) covalent geometry : bond 0.00194 ( 6720) covalent geometry : angle 0.54144 ( 9133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8077 (tppt) cc_final: 0.7062 (tttt) REVERT: A 586 ASP cc_start: 0.8002 (m-30) cc_final: 0.7628 (m-30) REVERT: B 41 LYS cc_start: 0.7985 (mtpt) cc_final: 0.6140 (tptt) REVERT: B 101 ILE cc_start: 0.8584 (mm) cc_final: 0.8336 (mm) REVERT: B 134 GLN cc_start: 0.6359 (tp40) cc_final: 0.5812 (pm20) REVERT: B 237 ARG cc_start: 0.7789 (mtm180) cc_final: 0.6561 (mtm-85) REVERT: H 159 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7721 (mt-10) REVERT: H 186 LEU cc_start: 0.8454 (mp) cc_final: 0.7798 (mt) REVERT: L 11 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7847 (tt) REVERT: L 17 GLU cc_start: 0.8253 (tp30) cc_final: 0.7922 (tp30) REVERT: L 168 ASP cc_start: 0.7640 (t0) cc_final: 0.7308 (t0) outliers start: 19 outliers final: 13 residues processed: 133 average time/residue: 0.1840 time to fit residues: 32.5902 Evaluate side-chains 129 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 0.0000 chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 139 ASN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.147482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104516 restraints weight = 8224.838| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.49 r_work: 0.3045 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6733 Z= 0.124 Angle : 0.577 9.833 9162 Z= 0.287 Chirality : 0.045 0.170 1023 Planarity : 0.006 0.089 1164 Dihedral : 5.890 50.242 950 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.89 % Allowed : 11.71 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.30), residues: 787 helix: -2.32 (0.82), residues: 26 sheet: 0.00 (0.33), residues: 269 loop : -1.84 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE B 238 TYR 0.015 0.001 TYR A 495 ARG 0.003 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 3.25238 ( 9) hydrogen bonds : bond 0.02739 ( 164) hydrogen bonds : angle 5.20107 ( 405) SS BOND : bond 0.00288 ( 10) SS BOND : angle 0.71595 ( 20) covalent geometry : bond 0.00292 ( 6720) covalent geometry : angle 0.56793 ( 9133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8146 (tppt) cc_final: 0.7178 (tttt) REVERT: A 586 ASP cc_start: 0.8071 (m-30) cc_final: 0.7724 (m-30) REVERT: B 41 LYS cc_start: 0.8073 (mtpt) cc_final: 0.6217 (tptt) REVERT: B 101 ILE cc_start: 0.8609 (mm) cc_final: 0.8357 (mm) REVERT: B 134 GLN cc_start: 0.6517 (tp40) cc_final: 0.5915 (pm20) REVERT: B 202 LYS cc_start: 0.8692 (mttp) cc_final: 0.8054 (mtpm) REVERT: B 237 ARG cc_start: 0.7859 (mtm180) cc_final: 0.6669 (mtm-85) REVERT: H 159 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7807 (mt-10) REVERT: L 11 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7955 (tt) REVERT: L 17 GLU cc_start: 0.8268 (tp30) cc_final: 0.7967 (tp30) REVERT: L 168 ASP cc_start: 0.7615 (t0) cc_final: 0.7362 (t0) outliers start: 21 outliers final: 18 residues processed: 127 average time/residue: 0.1896 time to fit residues: 31.8962 Evaluate side-chains 131 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 21 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 69.7941 > 50: distance: 8 - 9: 3.815 distance: 9 - 10: 25.859 distance: 9 - 12: 10.979 distance: 10 - 11: 7.535 distance: 10 - 16: 30.409 distance: 12 - 13: 10.246 distance: 13 - 14: 8.331 distance: 13 - 15: 8.993 distance: 16 - 17: 17.800 distance: 17 - 18: 33.674 distance: 17 - 20: 12.997 distance: 18 - 19: 34.911 distance: 18 - 23: 26.624 distance: 20 - 21: 10.906 distance: 20 - 22: 11.694 distance: 23 - 24: 16.290 distance: 24 - 25: 3.668 distance: 24 - 27: 13.715 distance: 25 - 26: 21.676 distance: 25 - 30: 25.594 distance: 27 - 28: 9.365 distance: 27 - 29: 10.371 distance: 30 - 31: 3.615 distance: 31 - 32: 26.592 distance: 31 - 34: 12.876 distance: 32 - 33: 15.611 distance: 32 - 44: 43.704 distance: 34 - 35: 17.078 distance: 35 - 36: 24.051 distance: 35 - 37: 11.294 distance: 36 - 38: 14.470 distance: 37 - 39: 9.697 distance: 37 - 40: 8.644 distance: 38 - 39: 11.473 distance: 39 - 41: 10.773 distance: 40 - 42: 10.434 distance: 41 - 43: 10.677 distance: 42 - 43: 12.068 distance: 44 - 45: 29.971 distance: 45 - 46: 11.059 distance: 45 - 48: 4.732 distance: 46 - 47: 10.498 distance: 46 - 55: 64.119 distance: 48 - 49: 24.886 distance: 49 - 50: 32.191 distance: 49 - 51: 18.637 distance: 51 - 53: 17.587 distance: 52 - 54: 27.012 distance: 53 - 54: 33.659 distance: 56 - 57: 38.581 distance: 56 - 59: 14.597 distance: 57 - 58: 3.088 distance: 59 - 60: 17.837 distance: 60 - 61: 27.224 distance: 60 - 62: 8.975 distance: 61 - 63: 19.257 distance: 62 - 64: 6.127 distance: 63 - 64: 36.819 distance: 65 - 66: 7.186 distance: 66 - 67: 10.681 distance: 66 - 69: 5.258 distance: 67 - 68: 12.172 distance: 67 - 73: 11.072 distance: 69 - 70: 8.047 distance: 70 - 71: 9.146 distance: 70 - 72: 7.942 distance: 73 - 74: 9.135 distance: 73 - 79: 32.062 distance: 74 - 75: 33.398 distance: 74 - 77: 28.539 distance: 75 - 76: 7.011 distance: 75 - 80: 27.023 distance: 77 - 78: 19.996 distance: 78 - 79: 9.723 distance: 80 - 81: 11.040 distance: 81 - 82: 27.196 distance: 81 - 84: 11.573 distance: 82 - 83: 35.095 distance: 82 - 87: 14.155 distance: 84 - 85: 39.341 distance: 84 - 86: 39.963 distance: 87 - 88: 30.325 distance: 87 - 121: 21.637 distance: 88 - 89: 41.655 distance: 88 - 91: 57.727 distance: 89 - 90: 13.217 distance: 89 - 95: 22.533 distance: 90 - 118: 29.407 distance: 91 - 92: 12.792 distance: 92 - 93: 46.271 distance: 92 - 94: 43.445