Starting phenix.real_space_refine on Sat Aug 3 08:59:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnu_12484/08_2024/7nnu_12484.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnu_12484/08_2024/7nnu_12484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnu_12484/08_2024/7nnu_12484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnu_12484/08_2024/7nnu_12484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnu_12484/08_2024/7nnu_12484.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nnu_12484/08_2024/7nnu_12484.cif" } resolution = 2.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5004 2.51 5 N 1266 2.21 5 O 1418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 145": "NH1" <-> "NH2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ASP 210": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7724 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2137 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 1 Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2131 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 12, 'TRANS': 260} Chain breaks: 1 Chain: "C" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1321 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "D" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2100 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 5.33, per 1000 atoms: 0.69 Number of scatterers: 7724 At special positions: 0 Unit cell: (87.894, 105.627, 100.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1418 8.00 N 1266 7.00 C 5004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 63.7% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 101 through 107 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 116 through 131 Processing helix chain 'A' and resid 133 through 137 removed outlier: 4.022A pdb=" N ALA A 137 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.188A pdb=" N VAL A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 194 removed outlier: 3.578A pdb=" N GLN A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.772A pdb=" N GLY A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 233 through 240 removed outlier: 4.098A pdb=" N LEU A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.578A pdb=" N LEU A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 4.119A pdb=" N ASN B 54 " --> pdb=" O MET B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.541A pdb=" N LEU B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.538A pdb=" N LEU B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.562A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 117 through 132 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.694A pdb=" N LEU B 146 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 177 through 194 Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 235 through 242 removed outlier: 3.737A pdb=" N LEU B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'C' and resid 12 through 31 Processing helix chain 'C' and resid 43 through 76 removed outlier: 3.930A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Proline residue: C 57 - end of helix Processing helix chain 'C' and resid 82 through 101 removed outlier: 3.769A pdb=" N THR C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 106 through 121 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 147 through 150 removed outlier: 3.652A pdb=" N MET C 150 " --> pdb=" O LEU C 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 150' Processing helix chain 'C' and resid 151 through 172 removed outlier: 3.869A pdb=" N ILE C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 165 " --> pdb=" O TRP C 161 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 170 " --> pdb=" O GLY C 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 removed outlier: 3.705A pdb=" N ARG D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 37 removed outlier: 3.581A pdb=" N LEU D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 59 removed outlier: 3.731A pdb=" N GLY D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 removed outlier: 4.036A pdb=" N PHE D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 87 Processing helix chain 'D' and resid 102 through 129 Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 152 through 184 Proline residue: D 168 - end of helix removed outlier: 3.714A pdb=" N ARG D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 Processing helix chain 'D' and resid 200 through 225 Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 245 through 263 removed outlier: 3.843A pdb=" N VAL D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 31 removed outlier: 6.791A pdb=" N SER A 24 " --> pdb=" O HIS A 10 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS A 10 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU A 26 " --> pdb=" O PHE A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.581A pdb=" N TRP A 35 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU A 214 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA A 37 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU A 216 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 39 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 213 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLN A 224 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 215 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 30 removed outlier: 6.198A pdb=" N ASP B 24 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER B 9 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 28 " --> pdb=" O PHE B 5 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL B 8 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER B 61 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.364A pdb=" N ILE B 167 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL B 201 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 169 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 36 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B 35 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU B 216 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA B 37 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU B 218 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 39 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU B 219 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 34 445 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 3.19 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: 2334 1.34 - 1.46: 1497 1.46 - 1.58: 3951 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 7850 Sorted by residual: bond pdb=" CG1 ILE C 74 " pdb=" CD1 ILE C 74 " ideal model delta sigma weight residual 1.513 1.390 0.123 3.90e-02 6.57e+02 9.95e+00 bond pdb=" CG LEU D 164 " pdb=" CD1 LEU D 164 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" CG LEU A 74 " pdb=" CD1 LEU A 74 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 bond pdb=" CB PRO D 202 " pdb=" CG PRO D 202 " ideal model delta sigma weight residual 1.492 1.411 0.081 5.00e-02 4.00e+02 2.61e+00 bond pdb=" CG PRO D 206 " pdb=" CD PRO D 206 " ideal model delta sigma weight residual 1.503 1.449 0.054 3.40e-02 8.65e+02 2.57e+00 ... (remaining 7845 not shown) Histogram of bond angle deviations from ideal: 96.31 - 103.92: 108 103.92 - 111.53: 3420 111.53 - 119.14: 3068 119.14 - 126.75: 3912 126.75 - 134.36: 122 Bond angle restraints: 10630 Sorted by residual: angle pdb=" C PHE A 13 " pdb=" N THR A 14 " pdb=" CA THR A 14 " ideal model delta sigma weight residual 121.70 128.15 -6.45 1.80e+00 3.09e-01 1.28e+01 angle pdb=" C LYS A 190 " pdb=" N GLU A 191 " pdb=" CA GLU A 191 " ideal model delta sigma weight residual 122.56 116.69 5.87 1.72e+00 3.38e-01 1.16e+01 angle pdb=" CA TRP B 128 " pdb=" CB TRP B 128 " pdb=" CG TRP B 128 " ideal model delta sigma weight residual 113.60 107.44 6.16 1.90e+00 2.77e-01 1.05e+01 angle pdb=" N GLN A 273 " pdb=" CA GLN A 273 " pdb=" CB GLN A 273 " ideal model delta sigma weight residual 110.16 114.85 -4.69 1.48e+00 4.57e-01 1.00e+01 angle pdb=" CB GLN A 277 " pdb=" CG GLN A 277 " pdb=" CD GLN A 277 " ideal model delta sigma weight residual 112.60 117.84 -5.24 1.70e+00 3.46e-01 9.50e+00 ... (remaining 10625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 4148 17.08 - 34.15: 438 34.15 - 51.22: 65 51.22 - 68.30: 11 68.30 - 85.37: 8 Dihedral angle restraints: 4670 sinusoidal: 1861 harmonic: 2809 Sorted by residual: dihedral pdb=" CA GLY C 80 " pdb=" C GLY C 80 " pdb=" N PHE C 81 " pdb=" CA PHE C 81 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ASP A 267 " pdb=" C ASP A 267 " pdb=" N ASP A 268 " pdb=" CA ASP A 268 " ideal model delta harmonic sigma weight residual -180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ARG D 184 " pdb=" C ARG D 184 " pdb=" N GLY D 185 " pdb=" CA GLY D 185 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1104 0.087 - 0.174: 120 0.174 - 0.261: 4 0.261 - 0.347: 0 0.347 - 0.434: 1 Chirality restraints: 1229 Sorted by residual: chirality pdb=" CB ILE A 6 " pdb=" CA ILE A 6 " pdb=" CG1 ILE A 6 " pdb=" CG2 ILE A 6 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CB ILE C 74 " pdb=" CA ILE C 74 " pdb=" CG1 ILE C 74 " pdb=" CG2 ILE C 74 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA GLU A 191 " pdb=" N GLU A 191 " pdb=" C GLU A 191 " pdb=" CB GLU A 191 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1226 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 97 " -0.011 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE A 97 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 97 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 97 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 97 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 97 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 97 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 177 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO B 178 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 72 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO B 73 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 73 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 73 " -0.039 5.00e-02 4.00e+02 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1738 2.78 - 3.31: 7290 3.31 - 3.84: 13828 3.84 - 4.37: 16660 4.37 - 4.90: 27732 Nonbonded interactions: 67248 Sorted by model distance: nonbonded pdb=" O VAL A 106 " pdb=" O HOH A 301 " model vdw 2.251 3.040 nonbonded pdb=" O LEU D 258 " pdb=" OG1 THR D 262 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP A 105 " pdb=" O HOH A 302 " model vdw 2.277 3.040 nonbonded pdb=" O PRO B 164 " pdb=" OH TYR B 191 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR A 12 " pdb=" OD2 ASP A 60 " model vdw 2.315 3.040 ... (remaining 67243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 7850 Z= 0.421 Angle : 0.794 7.660 10630 Z= 0.431 Chirality : 0.054 0.434 1229 Planarity : 0.007 0.071 1327 Dihedral : 14.015 85.373 2860 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 970 helix: -0.32 (0.20), residues: 570 sheet: 0.17 (0.63), residues: 61 loop : -0.45 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 128 HIS 0.004 0.001 HIS A 202 PHE 0.050 0.003 PHE A 97 TYR 0.016 0.002 TYR C 134 ARG 0.010 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.899 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.2064 time to fit residues: 205.3546 Evaluate side-chains 122 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 220 GLN B 7 ASN D 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7850 Z= 0.202 Angle : 0.554 6.177 10630 Z= 0.295 Chirality : 0.043 0.147 1229 Planarity : 0.006 0.066 1327 Dihedral : 4.694 15.941 1038 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.32 % Allowed : 8.65 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 970 helix: 0.99 (0.22), residues: 563 sheet: -0.31 (0.59), residues: 73 loop : -0.22 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 128 HIS 0.002 0.001 HIS A 202 PHE 0.011 0.001 PHE C 55 TYR 0.012 0.001 TYR C 134 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 229 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7616 (pt0) REVERT: A 271 LEU cc_start: 0.8577 (tp) cc_final: 0.8270 (tt) REVERT: A 274 SER cc_start: 0.8213 (t) cc_final: 0.7507 (p) REVERT: A 275 LEU cc_start: 0.8777 (mt) cc_final: 0.8559 (mt) REVERT: B 7 ASN cc_start: 0.7845 (t0) cc_final: 0.7452 (t0) REVERT: B 256 LEU cc_start: 0.8066 (mp) cc_final: 0.7861 (mp) REVERT: C 33 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.6803 (tttm) outliers start: 11 outliers final: 2 residues processed: 142 average time/residue: 1.1572 time to fit residues: 174.4517 Evaluate side-chains 131 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain C residue 33 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 91 GLN C 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7850 Z= 0.268 Angle : 0.559 6.387 10630 Z= 0.295 Chirality : 0.045 0.149 1229 Planarity : 0.005 0.059 1327 Dihedral : 4.612 16.534 1038 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.04 % Allowed : 10.46 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.27), residues: 970 helix: 1.37 (0.22), residues: 563 sheet: -0.48 (0.63), residues: 62 loop : -0.11 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 128 HIS 0.002 0.001 HIS A 10 PHE 0.011 0.002 PHE B 35 TYR 0.015 0.002 TYR D 251 ARG 0.007 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 229 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: B 7 ASN cc_start: 0.7769 (t0) cc_final: 0.7354 (t0) REVERT: C 33 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.6897 (tttm) REVERT: D 142 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8070 (mtt) REVERT: D 240 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7202 (mm-30) outliers start: 17 outliers final: 7 residues processed: 139 average time/residue: 1.1423 time to fit residues: 168.3555 Evaluate side-chains 136 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 91 GLN A 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7850 Z= 0.188 Angle : 0.517 9.226 10630 Z= 0.271 Chirality : 0.043 0.146 1229 Planarity : 0.005 0.056 1327 Dihedral : 4.385 15.592 1038 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.40 % Allowed : 12.02 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 970 helix: 1.64 (0.22), residues: 566 sheet: -0.55 (0.59), residues: 73 loop : -0.08 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 128 HIS 0.002 0.000 HIS A 202 PHE 0.008 0.001 PHE C 61 TYR 0.013 0.001 TYR D 251 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.909 Fit side-chains REVERT: A 180 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: A 194 ASN cc_start: 0.8149 (t0) cc_final: 0.7750 (t0) REVERT: A 229 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: C 33 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.6901 (tttm) REVERT: D 66 TRP cc_start: 0.7508 (t-100) cc_final: 0.7019 (t-100) REVERT: D 142 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8051 (mtt) REVERT: D 148 LEU cc_start: 0.7022 (pp) cc_final: 0.6724 (mm) REVERT: D 240 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7212 (mm-30) outliers start: 20 outliers final: 7 residues processed: 145 average time/residue: 1.2019 time to fit residues: 184.8784 Evaluate side-chains 137 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 240 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 41 HIS A 91 GLN A 202 HIS B 7 ASN C 77 ASN D 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7850 Z= 0.225 Angle : 0.537 8.577 10630 Z= 0.280 Chirality : 0.044 0.155 1229 Planarity : 0.005 0.057 1327 Dihedral : 4.399 16.494 1038 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.88 % Allowed : 13.10 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 970 helix: 1.69 (0.22), residues: 566 sheet: -0.66 (0.58), residues: 73 loop : -0.10 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 276 HIS 0.003 0.001 HIS A 202 PHE 0.011 0.001 PHE B 252 TYR 0.015 0.002 TYR D 251 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 194 ASN cc_start: 0.8158 (t0) cc_final: 0.7768 (t0) REVERT: A 229 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: C 33 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6926 (tttm) REVERT: D 142 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8055 (mtt) REVERT: D 240 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7201 (mm-30) outliers start: 24 outliers final: 9 residues processed: 144 average time/residue: 1.1819 time to fit residues: 180.4687 Evaluate side-chains 136 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 240 GLU Chi-restraints excluded: chain D residue 249 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 41 HIS A 91 GLN A 202 HIS B 7 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7850 Z= 0.162 Angle : 0.501 8.563 10630 Z= 0.264 Chirality : 0.042 0.141 1229 Planarity : 0.005 0.056 1327 Dihedral : 4.182 14.066 1038 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.52 % Allowed : 13.82 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.27), residues: 970 helix: 1.88 (0.22), residues: 565 sheet: -0.60 (0.59), residues: 73 loop : -0.13 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 276 HIS 0.002 0.000 HIS B 242 PHE 0.009 0.001 PHE C 61 TYR 0.012 0.001 TYR D 251 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 0.933 Fit side-chains REVERT: A 194 ASN cc_start: 0.8147 (t0) cc_final: 0.7767 (t0) REVERT: A 229 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: D 66 TRP cc_start: 0.7449 (t-100) cc_final: 0.6821 (t-100) REVERT: D 240 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7241 (mm-30) outliers start: 21 outliers final: 8 residues processed: 144 average time/residue: 1.1155 time to fit residues: 170.7414 Evaluate side-chains 139 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 240 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 0.0370 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 91 GLN A 202 HIS C 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7850 Z= 0.215 Angle : 0.528 8.613 10630 Z= 0.274 Chirality : 0.043 0.141 1229 Planarity : 0.005 0.056 1327 Dihedral : 4.244 17.270 1038 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.92 % Allowed : 14.66 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 970 helix: 1.89 (0.22), residues: 565 sheet: -0.52 (0.59), residues: 73 loop : -0.07 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 276 HIS 0.002 0.001 HIS A 202 PHE 0.009 0.001 PHE B 252 TYR 0.016 0.002 TYR C 53 ARG 0.007 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 194 ASN cc_start: 0.8177 (t0) cc_final: 0.7786 (t0) REVERT: A 229 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: D 66 TRP cc_start: 0.7471 (t-100) cc_final: 0.6827 (t-100) REVERT: D 142 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8037 (mtt) REVERT: D 148 LEU cc_start: 0.6947 (pp) cc_final: 0.6548 (mm) REVERT: D 240 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7226 (mm-30) outliers start: 16 outliers final: 8 residues processed: 141 average time/residue: 1.0866 time to fit residues: 163.1564 Evaluate side-chains 138 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 240 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4211 > 50: distance: 3 - 18: 3.066 distance: 26 - 47: 35.222 distance: 32 - 58: 38.021 distance: 40 - 66: 27.955 distance: 43 - 47: 35.128 distance: 48 - 49: 44.325 distance: 48 - 51: 37.282 distance: 49 - 50: 46.352 distance: 49 - 58: 29.802 distance: 51 - 52: 22.083 distance: 52 - 53: 14.204 distance: 52 - 54: 41.136 distance: 53 - 55: 57.488 distance: 54 - 56: 7.110 distance: 55 - 57: 25.119 distance: 56 - 57: 32.078 distance: 58 - 59: 39.493 distance: 59 - 60: 25.130 distance: 59 - 62: 24.348 distance: 60 - 61: 46.282 distance: 60 - 66: 24.599 distance: 62 - 63: 51.408 distance: 63 - 64: 43.100 distance: 63 - 65: 19.624 distance: 66 - 67: 15.456 distance: 67 - 68: 6.552 distance: 67 - 70: 3.734 distance: 68 - 69: 41.151 distance: 68 - 78: 43.830 distance: 70 - 71: 22.379 distance: 71 - 72: 19.741 distance: 71 - 73: 19.797 distance: 72 - 74: 8.132 distance: 73 - 75: 36.457 distance: 74 - 76: 30.698 distance: 75 - 76: 22.919 distance: 76 - 77: 41.939 distance: 78 - 79: 24.714 distance: 79 - 80: 23.460 distance: 79 - 82: 40.784 distance: 80 - 81: 24.833 distance: 80 - 87: 52.260 distance: 82 - 83: 29.291 distance: 83 - 84: 6.420 distance: 84 - 85: 22.394 distance: 85 - 86: 42.539 distance: 87 - 88: 13.437 distance: 88 - 89: 41.407 distance: 88 - 91: 23.023 distance: 89 - 90: 41.119 distance: 89 - 96: 56.163 distance: 91 - 92: 21.607 distance: 92 - 93: 20.133 distance: 93 - 94: 36.849 distance: 93 - 95: 55.419 distance: 96 - 97: 55.554 distance: 96 - 102: 54.736 distance: 97 - 98: 39.334 distance: 97 - 100: 50.666 distance: 98 - 99: 40.616 distance: 98 - 103: 11.413 distance: 100 - 101: 32.234 distance: 101 - 102: 38.929 distance: 103 - 104: 5.486 distance: 104 - 105: 16.664 distance: 104 - 107: 50.851 distance: 105 - 111: 36.529 distance: 107 - 108: 41.481 distance: 107 - 109: 14.844 distance: 111 - 112: 39.469 distance: 112 - 113: 43.911 distance: 112 - 115: 40.965 distance: 113 - 114: 31.735 distance: 113 - 120: 39.188 distance: 114 - 153: 31.401 distance: 115 - 116: 25.617 distance: 116 - 117: 32.266 distance: 117 - 118: 32.564 distance: 117 - 119: 10.096 distance: 120 - 121: 11.995 distance: 121 - 122: 24.498 distance: 121 - 124: 22.460 distance: 122 - 123: 37.696 distance: 122 - 128: 40.901 distance: 123 - 160: 29.910 distance: 124 - 125: 27.949 distance: 124 - 126: 43.880 distance: 125 - 127: 26.927 distance: 129 - 130: 27.212 distance: 129 - 132: 15.070 distance: 130 - 131: 48.815 distance: 130 - 142: 21.301 distance: 131 - 168: 34.721 distance: 132 - 133: 40.633 distance: 133 - 134: 21.149 distance: 133 - 135: 31.082 distance: 134 - 136: 12.760 distance: 135 - 137: 16.552 distance: 135 - 138: 22.325 distance: 136 - 137: 14.659 distance: 137 - 139: 6.150 distance: 138 - 140: 4.080 distance: 139 - 141: 22.740 distance: 140 - 141: 19.197