Starting phenix.real_space_refine on Tue May 13 22:39:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7y_36053/05_2025/8j7y_36053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7y_36053/05_2025/8j7y_36053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7y_36053/05_2025/8j7y_36053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7y_36053/05_2025/8j7y_36053.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7y_36053/05_2025/8j7y_36053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7y_36053/05_2025/8j7y_36053.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 46 5.16 5 C 7044 2.51 5 N 1830 2.21 5 O 2086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11008 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2193 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, B, F Time building chain proxies: 7.16, per 1000 atoms: 0.65 Number of scatterers: 11008 At special positions: 0 Unit cell: (76.7, 116.82, 159.3, 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) Zn 2 29.99 S 46 16.00 O 2086 8.00 N 1830 7.00 C 7044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " 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: 2.78 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 240 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 240 " 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 26 sheets defined 31.3% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.986A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 57 Processing helix chain 'A' and resid 61 through 88 removed outlier: 4.222A pdb=" N SER A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 132 Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 232 through 259 Processing helix chain 'A' and resid 267 through 294 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 303 through 314 removed outlier: 4.475A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.527A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.986A pdb=" N ARG B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 57 Processing helix chain 'B' and resid 61 through 88 removed outlier: 4.222A pdb=" N SER B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 132 Processing helix chain 'B' and resid 143 through 159 Processing helix chain 'B' and resid 232 through 259 Processing helix chain 'B' and resid 267 through 294 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 303 through 314 removed outlier: 4.475A pdb=" N GLN B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.527A pdb=" N ALA D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 328 removed outlier: 5.558A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 366 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.666A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.861A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.861A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.856A pdb=" N CYS E 200 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS E 213 " --> pdb=" O CYS E 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AB3, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.818A pdb=" N ASN C 141 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 137 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.659A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.666A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F 40 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.862A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.862A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 156 through 159 removed outlier: 3.856A pdb=" N CYS F 200 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 213 " --> pdb=" O CYS F 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 318 through 328 removed outlier: 5.558A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 366 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.819A pdb=" N ASN D 141 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 157 through 159 removed outlier: 4.660A pdb=" N TRP D 152 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS D 202 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER D 207 " --> pdb=" O HIS D 202 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1716 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: 4.18 Time building geometry restraints manager: 3.25 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: 3484 1.34 - 1.46: 2685 1.46 - 1.58: 5033 1.58 - 1.70: 0 1.70 - 1.81: 66 Bond restraints: 11268 Sorted by residual: bond pdb=" CG PRO C 145 " pdb=" CD PRO C 145 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.13e-01 bond pdb=" C ASP A 267 " pdb=" N PRO A 268 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.51e-01 bond pdb=" CG PRO D 145 " pdb=" CD PRO D 145 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.42e-01 bond pdb=" C ASP B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.18e-01 bond pdb=" CG PRO C 99 " pdb=" CD PRO C 99 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.08e-01 ... (remaining 11263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 15014 1.40 - 2.80: 255 2.80 - 4.21: 53 4.21 - 5.61: 10 5.61 - 7.01: 10 Bond angle restraints: 15342 Sorted by residual: angle pdb=" C VAL E 188 " pdb=" CA VAL E 188 " pdb=" CB VAL E 188 " ideal model delta sigma weight residual 109.33 112.33 -3.00 9.80e-01 1.04e+00 9.39e+00 angle pdb=" C VAL F 188 " pdb=" CA VAL F 188 " pdb=" CB VAL F 188 " ideal model delta sigma weight residual 109.33 112.33 -3.00 9.80e-01 1.04e+00 9.37e+00 angle pdb=" CA VAL F 188 " pdb=" C VAL F 188 " pdb=" N PRO F 189 " ideal model delta sigma weight residual 116.57 119.43 -2.86 9.80e-01 1.04e+00 8.55e+00 angle pdb=" CA VAL E 188 " pdb=" C VAL E 188 " pdb=" N PRO E 189 " ideal model delta sigma weight residual 116.57 119.40 -2.83 9.80e-01 1.04e+00 8.37e+00 angle pdb=" CA LYS C 153 " pdb=" CB LYS C 153 " pdb=" CG LYS C 153 " ideal model delta sigma weight residual 114.10 119.54 -5.44 2.00e+00 2.50e-01 7.40e+00 ... (remaining 15337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6097 17.88 - 35.77: 463 35.77 - 53.65: 72 53.65 - 71.54: 20 71.54 - 89.42: 8 Dihedral angle restraints: 6660 sinusoidal: 2526 harmonic: 4134 Sorted by residual: dihedral pdb=" CB CYS F 145 " pdb=" SG CYS F 145 " pdb=" SG CYS F 200 " pdb=" CB CYS F 200 " ideal model delta sinusoidal sigma weight residual 93.00 149.76 -56.76 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 149.73 -56.73 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 57.45 35.55 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 6657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1107 0.029 - 0.057: 406 0.057 - 0.086: 144 0.086 - 0.115: 94 0.115 - 0.144: 15 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE F 92 " pdb=" N ILE F 92 " pdb=" C ILE F 92 " pdb=" CB ILE F 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ASN B 152 " pdb=" N ASN B 152 " pdb=" C ASN B 152 " pdb=" CB ASN B 152 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1763 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 153 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO F 154 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 154 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 154 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 153 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO E 154 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 154 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 154 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 188 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO F 189 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " -0.023 5.00e-02 4.00e+02 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 62 2.51 - 3.11: 8088 3.11 - 3.71: 16902 3.71 - 4.30: 23705 4.30 - 4.90: 40316 Nonbonded interactions: 89073 Sorted by model distance: nonbonded pdb=" CG ASP A 74 " pdb="ZN ZN A 501 " model vdw 1.914 2.460 nonbonded pdb=" CG ASP B 74 " pdb="ZN ZN B 501 " model vdw 1.914 2.460 nonbonded pdb=" OD1 ASP A 74 " pdb="ZN ZN A 501 " model vdw 2.008 2.230 nonbonded pdb=" OD1 ASP B 74 " pdb="ZN ZN B 501 " model vdw 2.009 2.230 nonbonded pdb=" OD2 ASP B 244 " pdb="ZN ZN B 501 " model vdw 2.063 2.230 ... (remaining 89068 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: 0.06 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.670 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 0.106 11278 Z= 0.108 Angle : 0.504 7.010 15358 Z= 0.261 Chirality : 0.040 0.144 1766 Planarity : 0.003 0.050 1938 Dihedral : 13.140 89.420 3968 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.16 % Allowed : 0.33 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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 (0.23), residues: 1402 helix: 2.44 (0.25), residues: 422 sheet: 0.89 (0.25), residues: 470 loop : -0.29 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 152 HIS 0.009 0.001 HIS A 240 PHE 0.005 0.001 PHE C 102 TYR 0.017 0.001 TYR E 101 ARG 0.001 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.17616 ( 584) hydrogen bonds : angle 6.85440 ( 1716) metal coordination : bond 0.10579 ( 2) SS BOND : bond 0.00214 ( 8) SS BOND : angle 0.32924 ( 16) covalent geometry : bond 0.00200 (11268) covalent geometry : angle 0.50462 (15342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8169 (pp20) cc_final: 0.7904 (pp20) REVERT: A 128 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 319 TYR cc_start: 0.7798 (m-80) cc_final: 0.7569 (m-80) REVERT: C 4 LEU cc_start: 0.8703 (mt) cc_final: 0.8475 (mt) REVERT: C 78 THR cc_start: 0.8820 (m) cc_final: 0.8502 (p) REVERT: C 79 ILE cc_start: 0.8362 (mt) cc_final: 0.8128 (mt) REVERT: C 151 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7564 (mmmt) REVERT: B 33 LYS cc_start: 0.9496 (pptt) cc_final: 0.9287 (tppt) REVERT: B 37 ASN cc_start: 0.9189 (m110) cc_final: 0.8798 (m-40) REVERT: B 50 PHE cc_start: 0.8885 (m-10) cc_final: 0.8529 (m-10) REVERT: B 73 PHE cc_start: 0.6674 (m-10) cc_final: 0.6469 (m-10) REVERT: B 120 PHE cc_start: 0.8059 (m-10) cc_final: 0.7826 (m-10) REVERT: B 154 ILE cc_start: 0.8674 (mm) cc_final: 0.8401 (mm) REVERT: B 257 MET cc_start: 0.5897 (tmm) cc_final: 0.5556 (ptm) REVERT: D 107 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7971 (mmmt) REVERT: D 151 LYS cc_start: 0.8290 (mtpp) cc_final: 0.8080 (mmmt) REVERT: D 179 MET cc_start: 0.8227 (ttp) cc_final: 0.7978 (ttp) outliers start: 2 outliers final: 0 residues processed: 322 average time/residue: 0.2014 time to fit residues: 93.6094 Evaluate side-chains 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.0370 chunk 106 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 295 GLN A 361 GLN C 57 ASN C 165 ASN F 73 ASN B 295 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.081221 restraints weight = 19826.597| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.41 r_work: 0.3060 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11278 Z= 0.169 Angle : 0.625 11.629 15358 Z= 0.326 Chirality : 0.045 0.182 1766 Planarity : 0.004 0.054 1938 Dihedral : 3.887 16.080 1520 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.47 % Allowed : 11.32 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.16 (0.22), residues: 1402 helix: 2.19 (0.25), residues: 424 sheet: 0.82 (0.24), residues: 460 loop : -0.43 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 152 HIS 0.005 0.001 HIS A 240 PHE 0.019 0.002 PHE B 359 TYR 0.015 0.002 TYR E 150 ARG 0.004 0.000 ARG F 66 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 584) hydrogen bonds : angle 4.76622 ( 1716) metal coordination : bond 0.00601 ( 2) SS BOND : bond 0.00585 ( 8) SS BOND : angle 1.12092 ( 16) covalent geometry : bond 0.00367 (11268) covalent geometry : angle 0.62381 (15342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8696 (t0) cc_final: 0.8214 (t0) REVERT: A 37 ASN cc_start: 0.9378 (m110) cc_final: 0.9092 (p0) REVERT: A 52 GLU cc_start: 0.8130 (pp20) cc_final: 0.7766 (pp20) REVERT: A 74 ASP cc_start: 0.7636 (m-30) cc_final: 0.7378 (m-30) REVERT: A 128 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 240 HIS cc_start: 0.8102 (t-90) cc_final: 0.7762 (t-90) REVERT: E 72 ASP cc_start: 0.8038 (t0) cc_final: 0.7827 (t0) REVERT: E 176 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7590 (tm-30) REVERT: E 212 ASP cc_start: 0.8527 (m-30) cc_final: 0.8320 (m-30) REVERT: C 37 MET cc_start: 0.8307 (tpp) cc_final: 0.8076 (tpp) REVERT: C 160 GLN cc_start: 0.8530 (mp10) cc_final: 0.8022 (mp10) REVERT: C 189 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7945 (mp0) REVERT: F 32 TYR cc_start: 0.8760 (m-80) cc_final: 0.8428 (m-80) REVERT: F 59 TYR cc_start: 0.8777 (m-10) cc_final: 0.8354 (m-10) REVERT: F 72 ASP cc_start: 0.8260 (t0) cc_final: 0.7639 (t0) REVERT: B 50 PHE cc_start: 0.9083 (m-10) cc_final: 0.8683 (m-10) REVERT: B 154 ILE cc_start: 0.8850 (mm) cc_final: 0.8607 (mm) REVERT: B 257 MET cc_start: 0.5984 (tmm) cc_final: 0.5768 (ttt) REVERT: D 194 ASN cc_start: 0.9106 (t0) cc_final: 0.8832 (t0) outliers start: 18 outliers final: 11 residues processed: 226 average time/residue: 0.2026 time to fit residues: 67.3994 Evaluate side-chains 190 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 102 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 201 ASN B 70 HIS D 160 GLN D 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.118468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.081899 restraints weight = 20098.316| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.83 r_work: 0.3072 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11278 Z= 0.153 Angle : 0.575 13.108 15358 Z= 0.296 Chirality : 0.043 0.157 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.826 14.807 1520 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.95 % Allowed : 12.54 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.19 (0.22), residues: 1402 helix: 2.20 (0.24), residues: 424 sheet: 0.86 (0.24), residues: 454 loop : -0.42 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 58 HIS 0.004 0.001 HIS B 240 PHE 0.026 0.001 PHE A 149 TYR 0.013 0.001 TYR C 190 ARG 0.004 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 584) hydrogen bonds : angle 4.42150 ( 1716) metal coordination : bond 0.00336 ( 2) SS BOND : bond 0.00427 ( 8) SS BOND : angle 0.75446 ( 16) covalent geometry : bond 0.00345 (11268) covalent geometry : angle 0.57451 (15342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8670 (t0) cc_final: 0.8176 (t0) REVERT: A 52 GLU cc_start: 0.7972 (pp20) cc_final: 0.7645 (pp20) REVERT: A 128 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7462 (mt-10) REVERT: A 288 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7678 (tm-30) REVERT: E 72 ASP cc_start: 0.8140 (t0) cc_final: 0.7800 (t0) REVERT: E 138 ASN cc_start: 0.9336 (p0) cc_final: 0.9029 (p0) REVERT: E 176 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7674 (tm-30) REVERT: C 83 GLU cc_start: 0.8527 (pt0) cc_final: 0.8249 (pt0) REVERT: F 43 LYS cc_start: 0.8992 (ptpt) cc_final: 0.8686 (ptpt) REVERT: B 50 PHE cc_start: 0.9061 (m-10) cc_final: 0.8715 (m-10) REVERT: B 74 ASP cc_start: 0.7478 (m-30) cc_final: 0.7111 (m-30) REVERT: B 128 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8596 (tm-30) REVERT: B 154 ILE cc_start: 0.8837 (mm) cc_final: 0.8610 (mm) REVERT: B 257 MET cc_start: 0.5877 (tmm) cc_final: 0.5548 (ttt) REVERT: D 169 ASP cc_start: 0.8760 (m-30) cc_final: 0.8537 (m-30) outliers start: 24 outliers final: 14 residues processed: 211 average time/residue: 0.2034 time to fit residues: 64.1828 Evaluate side-chains 188 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 104 optimal weight: 0.0000 chunk 32 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 123 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.118947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.082783 restraints weight = 19788.211| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.93 r_work: 0.3083 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11278 Z= 0.126 Angle : 0.561 7.976 15358 Z= 0.290 Chirality : 0.043 0.214 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.776 15.502 1520 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.47 % Allowed : 14.58 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.20 (0.22), residues: 1402 helix: 2.12 (0.25), residues: 428 sheet: 0.92 (0.24), residues: 452 loop : -0.41 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 58 HIS 0.004 0.001 HIS A 240 PHE 0.023 0.001 PHE A 149 TYR 0.014 0.001 TYR E 150 ARG 0.004 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 584) hydrogen bonds : angle 4.30416 ( 1716) metal coordination : bond 0.00319 ( 2) SS BOND : bond 0.00432 ( 8) SS BOND : angle 0.58433 ( 16) covalent geometry : bond 0.00284 (11268) covalent geometry : angle 0.56070 (15342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8544 (t0) cc_final: 0.8052 (t0) REVERT: A 52 GLU cc_start: 0.8027 (pp20) cc_final: 0.7705 (pp20) REVERT: A 128 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7455 (mt-10) REVERT: A 288 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7760 (tm-30) REVERT: E 72 ASP cc_start: 0.8163 (t0) cc_final: 0.7807 (t0) REVERT: E 138 ASN cc_start: 0.9332 (p0) cc_final: 0.9118 (p0) REVERT: E 176 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7890 (tm-30) REVERT: C 83 GLU cc_start: 0.8505 (pt0) cc_final: 0.8186 (pt0) REVERT: C 160 GLN cc_start: 0.8522 (pm20) cc_final: 0.8241 (mp10) REVERT: F 43 LYS cc_start: 0.8983 (ptpt) cc_final: 0.8655 (ptpt) REVERT: F 59 TYR cc_start: 0.9046 (m-10) cc_final: 0.8830 (m-10) REVERT: B 50 PHE cc_start: 0.9059 (m-10) cc_final: 0.8704 (m-10) REVERT: B 92 ASP cc_start: 0.9049 (p0) cc_final: 0.8771 (p0) REVERT: B 128 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8431 (tm-30) REVERT: B 154 ILE cc_start: 0.8776 (mm) cc_final: 0.8544 (mm) outliers start: 18 outliers final: 13 residues processed: 199 average time/residue: 0.1892 time to fit residues: 55.9570 Evaluate side-chains 184 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 169 HIS F 201 ASN D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.118329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.079575 restraints weight = 20407.374| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.55 r_work: 0.2966 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11278 Z= 0.177 Angle : 0.577 6.908 15358 Z= 0.301 Chirality : 0.044 0.257 1766 Planarity : 0.004 0.049 1938 Dihedral : 3.876 14.749 1520 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.55 % Allowed : 15.39 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % 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: 1.13 (0.22), residues: 1402 helix: 2.05 (0.25), residues: 428 sheet: 0.73 (0.24), residues: 464 loop : -0.30 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 108 HIS 0.005 0.001 HIS B 240 PHE 0.029 0.001 PHE B 238 TYR 0.016 0.001 TYR C 190 ARG 0.003 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 584) hydrogen bonds : angle 4.25433 ( 1716) metal coordination : bond 0.01190 ( 2) SS BOND : bond 0.00347 ( 8) SS BOND : angle 0.80249 ( 16) covalent geometry : bond 0.00403 (11268) covalent geometry : angle 0.57669 (15342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 1.223 Fit side-chains REVERT: A 32 ASP cc_start: 0.8613 (t0) cc_final: 0.8103 (t0) REVERT: A 52 GLU cc_start: 0.8108 (pp20) cc_final: 0.7731 (pp20) REVERT: A 128 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7476 (mt-10) REVERT: A 160 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7700 (mmtm) REVERT: A 288 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7894 (tm-30) REVERT: A 347 ASP cc_start: 0.8579 (t0) cc_final: 0.8358 (t0) REVERT: E 72 ASP cc_start: 0.8234 (t0) cc_final: 0.7791 (t0) REVERT: E 138 ASN cc_start: 0.9327 (p0) cc_final: 0.9106 (p0) REVERT: E 176 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7802 (tm-30) REVERT: C 160 GLN cc_start: 0.8504 (pm20) cc_final: 0.8081 (mp10) REVERT: F 59 TYR cc_start: 0.9242 (m-10) cc_final: 0.9024 (m-10) REVERT: F 72 ASP cc_start: 0.8375 (t0) cc_final: 0.8068 (t0) REVERT: F 181 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8998 (m) REVERT: B 50 PHE cc_start: 0.9079 (m-10) cc_final: 0.8701 (m-10) REVERT: B 92 ASP cc_start: 0.9006 (p0) cc_final: 0.8698 (p0) REVERT: B 118 THR cc_start: 0.9302 (m) cc_final: 0.9021 (t) REVERT: B 128 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8397 (tm-30) REVERT: B 153 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9000 (pp) REVERT: B 154 ILE cc_start: 0.8725 (mm) cc_final: 0.8435 (mm) outliers start: 19 outliers final: 14 residues processed: 201 average time/residue: 0.1971 time to fit residues: 58.7066 Evaluate side-chains 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.0351 > 50: distance: 55 - 89: 26.543 distance: 73 - 78: 34.684 distance: 78 - 218: 37.521 distance: 79 - 80: 25.888 distance: 79 - 82: 38.138 distance: 80 - 81: 4.712 distance: 80 - 86: 15.367 distance: 81 - 215: 30.741 distance: 82 - 83: 6.005 distance: 83 - 84: 13.862 distance: 83 - 85: 16.117 distance: 86 - 87: 5.926 distance: 87 - 88: 12.614 distance: 87 - 90: 11.712 distance: 88 - 89: 14.590 distance: 88 - 94: 14.681 distance: 90 - 91: 7.022 distance: 91 - 92: 15.459 distance: 91 - 93: 9.104 distance: 94 - 95: 27.245 distance: 94 - 200: 32.388 distance: 95 - 96: 7.202 distance: 95 - 98: 18.670 distance: 96 - 97: 9.309 distance: 96 - 102: 28.660 distance: 98 - 99: 13.093 distance: 99 - 100: 11.016 distance: 99 - 101: 6.482 distance: 102 - 103: 27.521 distance: 103 - 104: 6.311 distance: 103 - 106: 30.469 distance: 104 - 105: 8.270 distance: 104 - 113: 3.223 distance: 106 - 107: 26.856 distance: 107 - 108: 12.546 distance: 107 - 109: 10.728 distance: 108 - 110: 21.516 distance: 109 - 111: 21.127 distance: 110 - 112: 6.378 distance: 111 - 112: 16.963 distance: 113 - 114: 44.928 distance: 114 - 115: 13.717 distance: 115 - 116: 9.833 distance: 115 - 125: 16.588 distance: 118 - 119: 18.007 distance: 118 - 120: 37.461 distance: 119 - 121: 9.896 distance: 120 - 122: 12.801 distance: 121 - 123: 3.172 distance: 122 - 123: 34.728 distance: 123 - 124: 12.225 distance: 125 - 126: 26.817 distance: 125 - 131: 15.721 distance: 126 - 127: 15.104 distance: 126 - 129: 32.253 distance: 127 - 128: 19.652 distance: 127 - 132: 21.140 distance: 129 - 130: 40.394 distance: 130 - 131: 33.554 distance: 132 - 133: 16.817 distance: 133 - 134: 21.610 distance: 133 - 136: 17.010 distance: 134 - 135: 41.057 distance: 134 - 141: 40.839 distance: 136 - 137: 40.473 distance: 138 - 139: 29.153 distance: 139 - 140: 18.200 distance: 141 - 142: 42.682 distance: 142 - 143: 23.948 distance: 142 - 145: 46.248 distance: 143 - 149: 39.952 distance: 145 - 146: 17.926 distance: 146 - 147: 40.212 distance: 146 - 148: 7.929 distance: 149 - 150: 4.925 distance: 150 - 151: 14.941 distance: 151 - 152: 18.672 distance: 151 - 157: 13.812 distance: 153 - 154: 7.995 distance: 157 - 158: 33.701 distance: 157 - 237: 26.891 distance: 158 - 159: 18.984 distance: 158 - 161: 9.245 distance: 159 - 160: 32.022 distance: 159 - 165: 22.996 distance: 160 - 234: 24.314 distance: 161 - 162: 6.747 distance: 162 - 163: 9.553 distance: 162 - 164: 42.020