Starting phenix.real_space_refine on Thu Mar 13 03:33:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j23_35943/03_2025/8j23_35943.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j23_35943/03_2025/8j23_35943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j23_35943/03_2025/8j23_35943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j23_35943/03_2025/8j23_35943.map" model { file = "/net/cci-nas-00/data/ceres_data/8j23_35943/03_2025/8j23_35943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j23_35943/03_2025/8j23_35943.cif" } resolution = 3.2 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= 0.001 sd= 0.021 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 57 5.16 5 C 5494 2.51 5 N 1460 2.21 5 O 1585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8596 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2084 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Chain: "B" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1698 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "F" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Time building chain proxies: 5.33, per 1000 atoms: 0.62 Number of scatterers: 8596 At special positions: 0 Unit cell: (117.52, 109.2, 123.76, 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 57 16.00 O 1585 8.00 N 1460 7.00 C 5494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 37.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 4 through 38 removed outlier: 3.538A pdb=" N TYR A 14 " --> pdb=" O ILE A 10 " (cutoff:3.500A) Proline residue: A 23 - end of helix removed outlier: 3.527A pdb=" N GLY A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 61 removed outlier: 3.600A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.913A pdb=" N LYS A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 110 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.744A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 removed outlier: 3.791A pdb=" N GLY A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 144 " --> pdb=" O HIS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 204 Proline residue: A 177 - end of helix removed outlier: 3.746A pdb=" N ILE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Proline residue: A 190 - end of helix removed outlier: 3.726A pdb=" N ARG A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 247 removed outlier: 3.581A pdb=" N ARG A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.840A pdb=" N HIS A 241 " --> pdb=" O TYR A 237 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 274 removed outlier: 3.663A pdb=" N VAL A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Proline residue: A 269 - end of helix removed outlier: 3.623A pdb=" N PHE A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.709A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.287A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.749A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.786A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 330 through 350 removed outlier: 3.691A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'D' and resid 2 through 20 Processing helix chain 'D' and resid 25 through 40 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.000A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190 removed outlier: 9.231A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 44 through 49 removed outlier: 5.872A pdb=" N THR C 45 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN C 338 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG C 47 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 334 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 61 removed outlier: 3.544A pdb=" N ALA C 58 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 72 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP C 81 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS C 87 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 98 through 103 removed outlier: 7.029A pdb=" N GLY C 113 " --> pdb=" O MET C 99 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS C 101 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA C 111 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR C 103 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR C 109 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS C 119 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU C 136 " --> pdb=" O CYS C 119 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 121 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 149 removed outlier: 3.719A pdb=" N THR C 176 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP C 168 " --> pdb=" O GLN C 174 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLN C 174 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 185 through 190 removed outlier: 3.588A pdb=" N PHE C 197 " --> pdb=" O TRP C 209 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN C 218 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ASP C 210 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS C 216 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 232 removed outlier: 3.620A pdb=" N LEU C 250 " --> pdb=" O MET C 260 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET C 260 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP C 252 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU C 258 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.833A pdb=" N SER C 273 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN C 291 " --> pdb=" O TYR C 287 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY C 304 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP C 296 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG C 302 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.585A pdb=" N THR F 115 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR F 94 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR F 50 " --> pdb=" O TYR F 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.585A pdb=" N THR F 115 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR F 94 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG F 98 " --> pdb=" O PHE F 110 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE F 110 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 132 through 135 Processing sheet with id=AB4, first strand: chain 'F' and resid 142 through 146 Processing sheet with id=AB5, first strand: chain 'F' and resid 180 through 181 removed outlier: 6.520A pdb=" N TRP F 162 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR F 176 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU F 160 " --> pdb=" O TYR F 176 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1182 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: 2.44 Time building geometry restraints manager: 2.36 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: 2763 1.34 - 1.46: 2144 1.46 - 1.58: 3797 1.58 - 1.70: 0 1.70 - 1.81: 81 Bond restraints: 8785 Sorted by residual: bond pdb=" CB PRO A 123 " pdb=" CG PRO A 123 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.38e+00 bond pdb=" CA TYR F 221 " pdb=" C TYR F 221 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.26e-02 6.30e+03 1.89e+00 bond pdb=" CG PRO A 123 " pdb=" CD PRO A 123 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.69e+00 bond pdb=" CB PRO F 222 " pdb=" CG PRO F 222 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.66e+00 bond pdb=" CB ASN C 235 " pdb=" CG ASN C 235 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 ... (remaining 8780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 11889 4.40 - 8.81: 18 8.81 - 13.21: 4 13.21 - 17.62: 0 17.62 - 22.02: 1 Bond angle restraints: 11912 Sorted by residual: angle pdb=" N TYR F 221 " pdb=" CA TYR F 221 " pdb=" C TYR F 221 " ideal model delta sigma weight residual 109.81 131.83 -22.02 2.21e+00 2.05e-01 9.93e+01 angle pdb=" C TYR F 221 " pdb=" N PRO F 222 " pdb=" CA PRO F 222 " ideal model delta sigma weight residual 119.84 132.25 -12.41 1.25e+00 6.40e-01 9.85e+01 angle pdb=" C PRO F 222 " pdb=" CA PRO F 222 " pdb=" CB PRO F 222 " ideal model delta sigma weight residual 111.56 124.71 -13.15 1.65e+00 3.67e-01 6.35e+01 angle pdb=" CA PRO F 222 " pdb=" N PRO F 222 " pdb=" CD PRO F 222 " ideal model delta sigma weight residual 112.00 106.05 5.95 1.40e+00 5.10e-01 1.80e+01 angle pdb=" C GLU F 220 " pdb=" N TYR F 221 " pdb=" CA TYR F 221 " ideal model delta sigma weight residual 121.80 130.60 -8.80 2.44e+00 1.68e-01 1.30e+01 ... (remaining 11907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 4690 24.81 - 49.62: 453 49.62 - 74.43: 31 74.43 - 99.25: 7 99.25 - 124.06: 1 Dihedral angle restraints: 5182 sinusoidal: 1995 harmonic: 3187 Sorted by residual: dihedral pdb=" CA TYR F 221 " pdb=" C TYR F 221 " pdb=" N PRO F 222 " pdb=" CA PRO F 222 " ideal model delta harmonic sigma weight residual 180.00 55.94 124.06 0 5.00e+00 4.00e-02 6.16e+02 dihedral pdb=" N TYR F 221 " pdb=" C TYR F 221 " pdb=" CA TYR F 221 " pdb=" CB TYR F 221 " ideal model delta harmonic sigma weight residual 122.80 158.56 -35.76 0 2.50e+00 1.60e-01 2.05e+02 dihedral pdb=" C TYR F 221 " pdb=" N TYR F 221 " pdb=" CA TYR F 221 " pdb=" CB TYR F 221 " ideal model delta harmonic sigma weight residual -122.60 -158.33 35.73 0 2.50e+00 1.60e-01 2.04e+02 ... (remaining 5179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 1347 0.326 - 0.653: 0 0.653 - 0.979: 1 0.979 - 1.306: 0 1.306 - 1.632: 1 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA TYR F 221 " pdb=" N TYR F 221 " pdb=" C TYR F 221 " pdb=" CB TYR F 221 " both_signs ideal model delta sigma weight residual False 2.51 0.88 1.63 2.00e-01 2.50e+01 6.66e+01 chirality pdb=" CA PRO F 222 " pdb=" N PRO F 222 " pdb=" C PRO F 222 " pdb=" CB PRO F 222 " both_signs ideal model delta sigma weight residual False 2.72 1.94 0.77 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" CA ILE F 100 " pdb=" N ILE F 100 " pdb=" C ILE F 100 " pdb=" CB ILE F 100 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 1346 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 122 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.10e+01 pdb=" N PRO A 123 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 233 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO C 234 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 221 " -0.062 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO F 222 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO F 222 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO F 222 " -0.042 5.00e-02 4.00e+02 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 150 2.67 - 3.23: 7875 3.23 - 3.79: 13577 3.79 - 4.34: 18090 4.34 - 4.90: 30431 Nonbonded interactions: 70123 Sorted by model distance: nonbonded pdb=" OG1 THR C 84 " pdb=" OD1 ASN C 86 " model vdw 2.116 3.040 nonbonded pdb=" O ILE C 56 " pdb=" OG SER C 314 " model vdw 2.183 3.040 nonbonded pdb=" OG SER C 106 " pdb=" OD1 ASN C 108 " model vdw 2.229 3.040 nonbonded pdb=" OG SER C 159 " pdb=" OD1 ASP C 161 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR C 63 " pdb=" O PRO C 105 " model vdw 2.265 3.040 ... (remaining 70118 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=0.02 max=1.00 mean=0.99 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: 0.010 Normalize map: mean=0, sd=1: 0.670 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.550 Find NCS groups from input model: 0.110 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 0.077 8785 Z= 0.151 Angle : 0.570 22.025 11912 Z= 0.295 Chirality : 0.062 1.632 1349 Planarity : 0.006 0.115 1504 Dihedral : 17.342 124.058 3125 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.49 % Rotamer: Outliers : 0.43 % Allowed : 30.60 % Favored : 68.97 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1083 helix: 1.42 (0.27), residues: 375 sheet: 0.86 (0.33), residues: 259 loop : -0.50 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 75 HIS 0.002 0.000 HIS F 35 PHE 0.028 0.001 PHE B 334 TYR 0.044 0.001 TYR F 221 ARG 0.004 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 VAL cc_start: 0.8069 (m) cc_final: 0.7806 (p) REVERT: A 249 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.5969 (tptm) REVERT: B 197 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7400 (mttp) REVERT: B 209 LYS cc_start: 0.7441 (ptmt) cc_final: 0.7174 (ptpp) REVERT: D 17 MET cc_start: 0.6721 (mmp) cc_final: 0.6513 (mmp) REVERT: F 39 GLN cc_start: 0.7687 (tt0) cc_final: 0.7451 (tt0) REVERT: F 126 MET cc_start: 0.7862 (tpp) cc_final: 0.7352 (tpp) outliers start: 4 outliers final: 1 residues processed: 216 average time/residue: 0.2342 time to fit residues: 67.5516 Evaluate side-chains 205 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain B residue 187 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 264 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 ASN F 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.148242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130324 restraints weight = 12015.780| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.12 r_work: 0.3484 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8785 Z= 0.287 Angle : 0.622 14.197 11912 Z= 0.325 Chirality : 0.045 0.318 1349 Planarity : 0.006 0.076 1504 Dihedral : 4.319 40.777 1195 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 5.71 % Allowed : 25.00 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.26), residues: 1083 helix: 1.55 (0.27), residues: 391 sheet: 0.82 (0.33), residues: 258 loop : -0.40 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 75 HIS 0.005 0.001 HIS C 89 PHE 0.021 0.002 PHE B 259 TYR 0.019 0.002 TYR F 59 ARG 0.008 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.896 Fit side-chains REVERT: A 119 LEU cc_start: 0.7080 (pt) cc_final: 0.6644 (pp) REVERT: A 184 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6202 (tt) REVERT: A 186 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7223 (tp) REVERT: A 267 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7227 (tt) REVERT: A 270 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7285 (tt) REVERT: A 273 TYR cc_start: 0.5006 (OUTLIER) cc_final: 0.4258 (p90) REVERT: B 46 LYS cc_start: 0.6733 (OUTLIER) cc_final: 0.6357 (mttp) REVERT: B 197 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7684 (mtpp) REVERT: B 209 LYS cc_start: 0.7915 (ptmt) cc_final: 0.7713 (ptmt) REVERT: B 259 PHE cc_start: 0.8164 (m-10) cc_final: 0.7612 (m-80) REVERT: B 312 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7513 (mttp) REVERT: C 23 CYS cc_start: 0.7841 (m) cc_final: 0.7436 (m) REVERT: C 47 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7030 (mpt180) REVERT: C 66 ARG cc_start: 0.6713 (ttp-170) cc_final: 0.5960 (ttp80) REVERT: F 39 GLN cc_start: 0.8130 (tt0) cc_final: 0.7871 (tt0) outliers start: 53 outliers final: 23 residues processed: 245 average time/residue: 0.2213 time to fit residues: 72.5739 Evaluate side-chains 245 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 96 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN B 213 HIS ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120867 restraints weight = 12180.101| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.11 r_work: 0.3429 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8785 Z= 0.251 Angle : 0.583 10.856 11912 Z= 0.298 Chirality : 0.045 0.322 1349 Planarity : 0.005 0.069 1504 Dihedral : 4.289 30.677 1191 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.97 % Favored : 95.84 % Rotamer: Outliers : 5.17 % Allowed : 24.78 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1083 helix: 1.62 (0.27), residues: 396 sheet: 0.52 (0.31), residues: 273 loop : -0.41 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 75 HIS 0.005 0.001 HIS B 213 PHE 0.017 0.002 PHE C 197 TYR 0.016 0.002 TYR F 59 ARG 0.005 0.001 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6240 (tt) REVERT: A 270 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7580 (tt) REVERT: A 273 TYR cc_start: 0.5119 (OUTLIER) cc_final: 0.4295 (p90) REVERT: B 197 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7597 (mtpp) REVERT: B 209 LYS cc_start: 0.8023 (ptmt) cc_final: 0.7814 (ptmt) REVERT: B 298 GLU cc_start: 0.6157 (pt0) cc_final: 0.5869 (pt0) REVERT: B 312 LYS cc_start: 0.7887 (mtmm) cc_final: 0.7659 (mttm) REVERT: C 23 CYS cc_start: 0.7770 (m) cc_final: 0.7299 (m) REVERT: C 35 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7635 (tp) REVERT: C 43 MET cc_start: 0.8142 (mtp) cc_final: 0.7932 (mtt) REVERT: C 47 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7141 (mpt180) REVERT: C 168 ASP cc_start: 0.6985 (t0) cc_final: 0.6752 (t0) REVERT: C 208 LEU cc_start: 0.7901 (tp) cc_final: 0.7651 (tp) REVERT: C 264 HIS cc_start: 0.8876 (OUTLIER) cc_final: 0.8595 (t-90) REVERT: F 141 VAL cc_start: 0.7618 (p) cc_final: 0.7400 (m) outliers start: 48 outliers final: 26 residues processed: 235 average time/residue: 0.2182 time to fit residues: 69.0294 Evaluate side-chains 242 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 264 HIS Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 67.456 > 50: distance: 23 - 37: 22.679 distance: 27 - 45: 23.109 distance: 32 - 51: 12.095 distance: 35 - 37: 21.818 distance: 36 - 59: 22.879 distance: 37 - 38: 25.253 distance: 38 - 39: 30.744 distance: 38 - 41: 10.991 distance: 39 - 40: 11.635 distance: 39 - 45: 39.891 distance: 40 - 68: 37.734 distance: 41 - 42: 25.093 distance: 41 - 43: 20.856 distance: 42 - 44: 14.433 distance: 45 - 46: 21.277 distance: 46 - 47: 18.359 distance: 46 - 49: 21.520 distance: 47 - 48: 19.299 distance: 47 - 51: 23.338 distance: 48 - 79: 32.970 distance: 49 - 50: 24.040 distance: 51 - 52: 17.136 distance: 52 - 53: 15.243 distance: 52 - 55: 15.302 distance: 53 - 54: 10.034 distance: 53 - 59: 19.286 distance: 54 - 91: 27.433 distance: 55 - 56: 17.322 distance: 55 - 57: 15.513 distance: 59 - 60: 35.280 distance: 60 - 61: 48.758 distance: 60 - 63: 23.342 distance: 61 - 62: 30.904 distance: 61 - 68: 44.020 distance: 62 - 99: 32.206 distance: 63 - 64: 47.761 distance: 64 - 65: 25.303 distance: 65 - 66: 13.306 distance: 65 - 67: 9.396 distance: 68 - 69: 46.616 distance: 69 - 70: 62.841 distance: 69 - 72: 39.665 distance: 70 - 71: 49.444 distance: 70 - 79: 23.877 distance: 72 - 73: 34.154 distance: 73 - 74: 25.243 distance: 74 - 75: 11.118 distance: 75 - 76: 3.253 distance: 76 - 77: 6.792 distance: 76 - 78: 10.199 distance: 79 - 80: 18.895 distance: 80 - 81: 53.365 distance: 80 - 83: 36.312 distance: 81 - 82: 20.623 distance: 81 - 91: 44.514 distance: 83 - 84: 34.112 distance: 84 - 85: 21.575 distance: 84 - 86: 31.017 distance: 85 - 87: 15.591 distance: 86 - 88: 26.271 distance: 87 - 89: 6.742 distance: 88 - 89: 6.039 distance: 89 - 90: 4.699 distance: 91 - 92: 29.553 distance: 92 - 93: 54.964 distance: 92 - 95: 22.456 distance: 93 - 94: 55.230 distance: 95 - 96: 10.288 distance: 96 - 97: 7.926 distance: 96 - 98: 3.877 distance: 99 - 100: 47.884 distance: 100 - 101: 45.394 distance: 101 - 102: 42.457 distance: 101 - 103: 40.629 distance: 103 - 104: 24.639 distance: 104 - 105: 31.206 distance: 104 - 107: 28.211 distance: 105 - 106: 36.512 distance: 105 - 110: 40.665 distance: 107 - 108: 33.233 distance: 107 - 109: 30.681 distance: 110 - 111: 52.166 distance: 111 - 112: 42.081 distance: 111 - 114: 12.051 distance: 112 - 113: 43.690 distance: 112 - 115: 27.676