Starting phenix.real_space_refine on Mon Jun 16 17:45:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmj_41391/06_2025/8tmj_41391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmj_41391/06_2025/8tmj_41391.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/8tmj_41391/06_2025/8tmj_41391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmj_41391/06_2025/8tmj_41391.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmj_41391/06_2025/8tmj_41391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmj_41391/06_2025/8tmj_41391.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= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1577 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 3 5.21 5 S 65 5.16 5 C 11503 2.51 5 N 2895 2.21 5 O 3292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17758 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "A" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2909 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain: "C" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2804 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "D" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2935 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "E" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.40, per 1000 atoms: 0.59 Number of scatterers: 17758 At special positions: 0 Unit cell: (133.5, 134.568, 161.268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Mg 3 11.99 O 3292 8.00 N 2895 7.00 C 11503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 89 " distance=2.03 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: 4.29 Conformation dependent library (CDL) restraints added in 2.1 seconds 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4132 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 48.7% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'A' and resid 46 through 56 removed outlier: 3.576A pdb=" N SER A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 50 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.691A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.906A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.604A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 239 removed outlier: 4.107A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.830A pdb=" N VAL A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 284 removed outlier: 3.761A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 312 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 325 through 345 Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.602A pdb=" N ASP B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 56 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.676A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 238 Proline residue: B 227 - end of helix removed outlier: 4.253A pdb=" N ASP B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 310 removed outlier: 3.521A pdb=" N PHE B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 325 through 348 removed outlier: 3.788A pdb=" N LYS B 348 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 50 through 56 removed outlier: 4.175A pdb=" N ARG C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 50 through 56' Processing helix chain 'C' and resid 69 through 81 Processing helix chain 'C' and resid 83 through 92 removed outlier: 3.599A pdb=" N LEU C 87 " --> pdb=" O HIS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 165 through 202 removed outlier: 3.649A pdb=" N LEU C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 238 Proline residue: C 227 - end of helix removed outlier: 3.616A pdb=" N GLU C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 281 Processing helix chain 'C' and resid 284 through 310 removed outlier: 4.075A pdb=" N ASN C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 318 through 323 removed outlier: 4.226A pdb=" N ARG C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 348 removed outlier: 3.560A pdb=" N LYS C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.502A pdb=" N SER D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 51 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Proline residue: D 52 - end of helix removed outlier: 3.506A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.517A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 239 removed outlier: 4.462A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.921A pdb=" N VAL D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 removed outlier: 3.565A pdb=" N GLU D 244 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 312 removed outlier: 4.224A pdb=" N ASP D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.594A pdb=" N VAL D 329 " --> pdb=" O TRP D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.692A pdb=" N VAL E 50 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 51 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Proline residue: E 52 - end of helix Processing helix chain 'E' and resid 69 through 81 removed outlier: 4.164A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 165 through 202 removed outlier: 3.541A pdb=" N LEU E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 238 removed outlier: 3.815A pdb=" N TRP E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) Proline residue: E 227 - end of helix Processing helix chain 'E' and resid 247 through 311 Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 325 through 348 removed outlier: 4.105A pdb=" N VAL E 329 " --> pdb=" O TRP E 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR H 100 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N MET H 113 " --> pdb=" O TYR H 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.792A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 5 through 8 removed outlier: 3.563A pdb=" N THR G 23 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.781A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 3 through 7 removed outlier: 5.698A pdb=" N GLY F 16 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.576A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS F 96 " --> pdb=" O TRP F 116 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TRP F 116 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG F 98 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.576A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 39 through 44 removed outlier: 3.562A pdb=" N ILE A 29 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 98 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 39 through 44 removed outlier: 3.543A pdb=" N GLU B 125 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 106 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.668A pdb=" N ILE C 29 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 60 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N MET C 138 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE C 62 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLN C 140 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE C 64 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 128 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 39 through 44 removed outlier: 4.287A pdb=" N GLU D 121 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 123 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 28 through 33 removed outlier: 3.601A pdb=" N ILE E 64 " --> pdb=" O MET E 138 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU E 131 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL E 106 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS E 98 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 114 through 115 1098 hydrogen bonds defined for protein. 3147 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: 5.70 Time building geometry restraints manager: 4.87 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: 5571 1.34 - 1.46: 2867 1.46 - 1.57: 9607 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 18162 Sorted by residual: bond pdb=" CB VAL B 254 " pdb=" CG2 VAL B 254 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CG LYS E 117 " pdb=" CD LYS E 117 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.13e+00 bond pdb=" N PRO D 319 " pdb=" CA PRO D 319 " ideal model delta sigma weight residual 1.469 1.482 -0.013 1.28e-02 6.10e+03 1.09e+00 bond pdb=" CB THR D 20 " pdb=" CG2 THR D 20 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.00e+00 bond pdb=" CB LYS A 22 " pdb=" CG LYS A 22 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.00e+00 ... (remaining 18157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 24189 1.78 - 3.56: 343 3.56 - 5.35: 80 5.35 - 7.13: 17 7.13 - 8.91: 4 Bond angle restraints: 24633 Sorted by residual: angle pdb=" C LEU A 235 " pdb=" N TYR A 236 " pdb=" CA TYR A 236 " ideal model delta sigma weight residual 122.06 113.15 8.91 1.86e+00 2.89e-01 2.30e+01 angle pdb=" C VAL D 333 " pdb=" N MET D 334 " pdb=" CA MET D 334 " ideal model delta sigma weight residual 121.14 114.81 6.33 1.75e+00 3.27e-01 1.31e+01 angle pdb=" C LEU E 235 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " ideal model delta sigma weight residual 122.54 117.14 5.40 1.65e+00 3.67e-01 1.07e+01 angle pdb=" CB LYS E 117 " pdb=" CG LYS E 117 " pdb=" CD LYS E 117 " ideal model delta sigma weight residual 111.30 118.61 -7.31 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CB LYS C 349 " pdb=" CG LYS C 349 " pdb=" CD LYS C 349 " ideal model delta sigma weight residual 111.30 118.45 -7.15 2.30e+00 1.89e-01 9.68e+00 ... (remaining 24628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9661 17.95 - 35.91: 988 35.91 - 53.86: 174 53.86 - 71.82: 35 71.82 - 89.77: 22 Dihedral angle restraints: 10880 sinusoidal: 4473 harmonic: 6407 Sorted by residual: dihedral pdb=" CA PRO B 240 " pdb=" C PRO B 240 " pdb=" N PRO B 241 " pdb=" CA PRO B 241 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA VAL C 283 " pdb=" C VAL C 283 " pdb=" N SER C 284 " pdb=" CA SER C 284 " ideal model delta harmonic sigma weight residual 180.00 -158.69 -21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA SER C 284 " pdb=" C SER C 284 " pdb=" N ASN C 285 " pdb=" CA ASN C 285 " ideal model delta harmonic sigma weight residual 180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 10877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1717 0.031 - 0.063: 675 0.063 - 0.094: 249 0.094 - 0.126: 132 0.126 - 0.157: 15 Chirality restraints: 2788 Sorted by residual: chirality pdb=" CA PRO B 241 " pdb=" N PRO B 241 " pdb=" C PRO B 241 " pdb=" CB PRO B 241 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA GLU E 186 " pdb=" N GLU E 186 " pdb=" C GLU E 186 " pdb=" CB GLU E 186 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB VAL B 239 " pdb=" CA VAL B 239 " pdb=" CG1 VAL B 239 " pdb=" CG2 VAL B 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 2785 not shown) Planarity restraints: 3083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 202 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 203 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 327 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO B 328 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 240 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 241 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " -0.022 5.00e-02 4.00e+02 ... (remaining 3080 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 661 2.72 - 3.26: 18006 3.26 - 3.81: 28986 3.81 - 4.35: 35401 4.35 - 4.90: 60718 Nonbonded interactions: 143772 Sorted by model distance: nonbonded pdb=" OG SER G 92 " pdb=" OD1 ASN F 111 " model vdw 2.174 3.040 nonbonded pdb=" OE1 GLU D 196 " pdb=" NH1 ARG E 216 " model vdw 2.182 3.120 nonbonded pdb=" OD2 ASP B 145 " pdb=" NH2 ARG B 151 " model vdw 2.215 3.120 nonbonded pdb=" OH TYR E 19 " pdb=" OE1 GLU E 141 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR C 44 " pdb=" OD1 ASP C 46 " model vdw 2.246 3.040 ... (remaining 143767 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 350) selection = (chain 'B' and resid 17 through 350) selection = (chain 'C' and resid 17 through 350) selection = (chain 'D' and resid 17 through 350) selection = (chain 'E' and resid 17 through 350) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = (chain 'L' and resid 2 through 107) } 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=0.49 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: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.110 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.003 0.041 18166 Z= 0.152 Angle : 0.586 8.911 24641 Z= 0.306 Chirality : 0.043 0.157 2788 Planarity : 0.004 0.054 3083 Dihedral : 15.080 89.769 6736 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 2147 helix: 2.70 (0.16), residues: 942 sheet: 0.64 (0.24), residues: 487 loop : -1.08 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 350 HIS 0.003 0.001 HIS D 83 PHE 0.024 0.001 PHE A 306 TYR 0.020 0.001 TYR E 327 ARG 0.009 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.16068 ( 1074) hydrogen bonds : angle 6.61877 ( 3147) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.51901 ( 8) covalent geometry : bond 0.00346 (18162) covalent geometry : angle 0.58569 (24633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 2.210 Fit side-chains revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7176 (tp30) cc_final: 0.6873 (tp30) REVERT: G 25 ARG cc_start: 0.7562 (ttm170) cc_final: 0.6847 (ttm110) REVERT: G 104 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7673 (ttmm) REVERT: A 341 MET cc_start: 0.7406 (mmm) cc_final: 0.7022 (mmm) REVERT: B 259 ILE cc_start: 0.8841 (mt) cc_final: 0.8531 (mt) REVERT: B 263 ASP cc_start: 0.6735 (m-30) cc_final: 0.6502 (m-30) REVERT: C 112 MET cc_start: 0.7687 (mtp) cc_final: 0.7444 (mtm) REVERT: D 116 ASP cc_start: 0.7605 (t0) cc_final: 0.7104 (t0) REVERT: D 189 ASP cc_start: 0.7412 (t70) cc_final: 0.7123 (t70) REVERT: E 133 LYS cc_start: 0.7111 (ttmt) cc_final: 0.6548 (mttp) REVERT: E 138 MET cc_start: 0.7066 (mmp) cc_final: 0.6362 (mmp) REVERT: E 189 ASP cc_start: 0.7454 (t0) cc_final: 0.6746 (t0) REVERT: E 220 GLU cc_start: 0.7428 (tt0) cc_final: 0.7077 (tt0) REVERT: E 246 GLU cc_start: 0.7711 (mp0) cc_final: 0.7461 (mp0) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.2864 time to fit residues: 177.6440 Evaluate side-chains 359 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN A 140 GLN B 63 ASN B 140 GLN C 63 ASN C 134 ASN D 0 HIS D 95 GLN E 74 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.200482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.138702 restraints weight = 20909.180| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.51 r_work: 0.3180 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 18166 Z= 0.232 Angle : 0.643 8.632 24641 Z= 0.340 Chirality : 0.046 0.178 2788 Planarity : 0.005 0.050 3083 Dihedral : 4.453 24.082 2400 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 1.46 % Allowed : 9.53 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2147 helix: 2.58 (0.16), residues: 954 sheet: 0.57 (0.24), residues: 478 loop : -1.17 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 350 HIS 0.005 0.001 HIS D 94 PHE 0.021 0.002 PHE B 42 TYR 0.020 0.002 TYR D 236 ARG 0.009 0.001 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.06094 ( 1074) hydrogen bonds : angle 5.06737 ( 3147) SS BOND : bond 0.00360 ( 4) SS BOND : angle 1.03898 ( 8) covalent geometry : bond 0.00556 (18162) covalent geometry : angle 0.64323 (24633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 357 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7794 (tp30) cc_final: 0.7430 (tp30) REVERT: G 25 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7245 (ttm110) REVERT: F 114 ASP cc_start: 0.8813 (p0) cc_final: 0.8535 (p0) REVERT: A 152 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7060 (mt-10) REVERT: A 225 ILE cc_start: 0.8079 (tp) cc_final: 0.7667 (tp) REVERT: A 341 MET cc_start: 0.7652 (mmm) cc_final: 0.7362 (mmm) REVERT: B 148 ASP cc_start: 0.8425 (t0) cc_final: 0.8143 (t0) REVERT: B 263 ASP cc_start: 0.7924 (m-30) cc_final: 0.7594 (m-30) REVERT: B 291 MET cc_start: 0.7855 (mmp) cc_final: 0.7459 (mmp) REVERT: B 297 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7936 (mp) REVERT: C 152 GLU cc_start: 0.7863 (tt0) cc_final: 0.7553 (tt0) REVERT: D 189 ASP cc_start: 0.8281 (t70) cc_final: 0.7969 (t70) REVERT: E 34 TYR cc_start: 0.6145 (p90) cc_final: 0.5896 (p90) REVERT: E 138 MET cc_start: 0.7010 (mmp) cc_final: 0.6358 (mmp) REVERT: E 220 GLU cc_start: 0.8230 (tt0) cc_final: 0.7741 (tt0) REVERT: E 222 ARG cc_start: 0.7481 (ttt180) cc_final: 0.6856 (mtp180) REVERT: E 246 GLU cc_start: 0.7984 (mp0) cc_final: 0.7622 (mp0) REVERT: E 270 ASP cc_start: 0.7909 (m-30) cc_final: 0.7699 (m-30) outliers start: 29 outliers final: 24 residues processed: 371 average time/residue: 0.2805 time to fit residues: 160.6904 Evaluate side-chains 366 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 341 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 133 optimal weight: 0.5980 chunk 157 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.202381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.136254 restraints weight = 20884.915| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.17 r_work: 0.3175 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18166 Z= 0.158 Angle : 0.572 7.985 24641 Z= 0.302 Chirality : 0.043 0.158 2788 Planarity : 0.004 0.040 3083 Dihedral : 4.301 23.742 2400 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.83 % Rotamer: Outliers : 1.91 % Allowed : 12.34 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 2147 helix: 2.80 (0.16), residues: 953 sheet: 0.67 (0.24), residues: 470 loop : -1.14 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 350 HIS 0.003 0.001 HIS D 83 PHE 0.017 0.001 PHE A 27 TYR 0.021 0.001 TYR D 236 ARG 0.005 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.05486 ( 1074) hydrogen bonds : angle 4.69893 ( 3147) SS BOND : bond 0.00739 ( 4) SS BOND : angle 0.86860 ( 8) covalent geometry : bond 0.00360 (18162) covalent geometry : angle 0.57143 (24633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 367 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 GLU cc_start: 0.7553 (tp30) cc_final: 0.7184 (tp30) REVERT: G 25 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7176 (ttm110) REVERT: A 78 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: A 152 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6938 (mt-10) REVERT: A 225 ILE cc_start: 0.7962 (tp) cc_final: 0.7534 (tp) REVERT: A 341 MET cc_start: 0.7786 (mmm) cc_final: 0.7520 (mmm) REVERT: B 148 ASP cc_start: 0.8370 (t0) cc_final: 0.7985 (t0) REVERT: B 263 ASP cc_start: 0.7570 (m-30) cc_final: 0.7241 (m-30) REVERT: B 297 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7842 (mp) REVERT: C 30 GLU cc_start: 0.6620 (pt0) cc_final: 0.6397 (pt0) REVERT: C 98 LYS cc_start: 0.8064 (pttt) cc_final: 0.7858 (pttm) REVERT: C 152 GLU cc_start: 0.7680 (tt0) cc_final: 0.7316 (tt0) REVERT: D 189 ASP cc_start: 0.7916 (t70) cc_final: 0.7571 (t70) REVERT: E 32 MET cc_start: 0.4677 (ttt) cc_final: 0.4423 (tpt) REVERT: E 133 LYS cc_start: 0.6908 (ttmt) cc_final: 0.6359 (mmtm) REVERT: E 138 MET cc_start: 0.6870 (mmp) cc_final: 0.6209 (mmp) REVERT: E 220 GLU cc_start: 0.8030 (tt0) cc_final: 0.7485 (tt0) REVERT: E 222 ARG cc_start: 0.7223 (ttt180) cc_final: 0.6834 (ttp80) REVERT: E 246 GLU cc_start: 0.8027 (mp0) cc_final: 0.7711 (mp0) REVERT: E 292 LYS cc_start: 0.7793 (tttp) cc_final: 0.7421 (tptt) outliers start: 38 outliers final: 22 residues processed: 388 average time/residue: 0.2832 time to fit residues: 170.5044 Evaluate side-chains 368 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 344 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 287 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 57.3086 > 50: distance: 53 - 58: 20.304 distance: 58 - 59: 18.412 distance: 59 - 60: 10.129 distance: 60 - 61: 17.623 distance: 60 - 62: 16.946 distance: 62 - 63: 3.600 distance: 63 - 64: 14.294 distance: 63 - 66: 7.593 distance: 64 - 65: 12.059 distance: 64 - 70: 15.636 distance: 66 - 67: 16.074 distance: 67 - 68: 12.585 distance: 67 - 69: 25.820 distance: 70 - 71: 7.089 distance: 70 - 76: 16.050 distance: 71 - 72: 28.984 distance: 71 - 74: 28.345 distance: 72 - 73: 10.862 distance: 72 - 77: 17.363 distance: 74 - 75: 16.066 distance: 75 - 76: 24.668 distance: 77 - 78: 8.776 distance: 77 - 83: 16.637 distance: 78 - 79: 12.353 distance: 78 - 81: 38.024 distance: 79 - 80: 21.864 distance: 79 - 84: 20.750 distance: 81 - 82: 15.335 distance: 82 - 83: 28.435 distance: 84 - 85: 25.107 distance: 85 - 86: 25.022 distance: 86 - 87: 21.993 distance: 86 - 88: 25.763 distance: 88 - 89: 10.277 distance: 89 - 90: 15.799 distance: 89 - 92: 8.842 distance: 90 - 91: 13.459 distance: 90 - 95: 22.301 distance: 92 - 93: 15.177 distance: 92 - 94: 40.596 distance: 95 - 96: 23.043 distance: 96 - 97: 15.912 distance: 96 - 99: 12.811 distance: 97 - 98: 28.438 distance: 97 - 103: 6.482 distance: 99 - 100: 4.772 distance: 100 - 101: 11.578 distance: 100 - 102: 10.532 distance: 103 - 104: 7.759 distance: 104 - 105: 18.775 distance: 104 - 107: 17.119 distance: 105 - 106: 9.712 distance: 105 - 110: 9.778 distance: 107 - 108: 26.785 distance: 107 - 109: 5.360 distance: 110 - 111: 10.722 distance: 111 - 112: 4.577 distance: 111 - 114: 5.724 distance: 112 - 113: 5.810 distance: 112 - 122: 3.704 distance: 116 - 118: 4.114 distance: 120 - 121: 9.718 distance: 122 - 123: 11.003 distance: 123 - 124: 12.820 distance: 123 - 126: 28.923 distance: 124 - 125: 19.256 distance: 124 - 129: 18.951 distance: 126 - 127: 24.466