Starting phenix.real_space_refine on Mon Mar 11 13:14:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/03_2024/8grx_34216.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/03_2024/8grx_34216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/03_2024/8grx_34216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/03_2024/8grx_34216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/03_2024/8grx_34216.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grx_34216/03_2024/8grx_34216.pdb" } resolution = 3.0 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= 0.002 sd= 0.116 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 42 5.16 5 C 5256 2.51 5 N 1474 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 35": "OD1" <-> "OD2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "B PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 59": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 412": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8328 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1140 Classifications: {'peptide': 138} Link IDs: {'TRANS': 137} Chain breaks: 1 Chain: "B" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3024 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 352} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1140 Classifications: {'peptide': 138} Link IDs: {'TRANS': 137} Chain breaks: 1 Chain: "D" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3024 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 352} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.84, per 1000 atoms: 0.58 Number of scatterers: 8328 At special positions: 0 Unit cell: (124.063, 150.412, 77.9509, 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 42 16.00 O 1556 8.00 N 1474 7.00 C 5256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 245 " - pdb=" SG CYS B 296 " distance=2.02 Simple disulfide: pdb=" SG CYS B 345 " - pdb=" SG CYS B 396 " distance=2.04 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 245 " - pdb=" SG CYS D 296 " distance=2.02 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 396 " distance=2.04 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 22 sheets defined 27.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 23 through 43 removed outlier: 3.953A pdb=" N LEU A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 54 through 82 Processing helix chain 'A' and resid 87 through 125 Processing helix chain 'A' and resid 130 through 162 removed outlier: 3.543A pdb=" N ARG A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 171 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.619A pdb=" N ALA B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 43 removed outlier: 3.953A pdb=" N LEU C 43 " --> pdb=" O TRP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 54 through 82 Processing helix chain 'C' and resid 87 through 125 Processing helix chain 'C' and resid 130 through 162 removed outlier: 3.543A pdb=" N ARG C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.619A pdb=" N ALA D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39 removed outlier: 6.525A pdb=" N MET B 117 " --> pdb=" O TRP B 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU B 57 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU B 57 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.213A pdb=" N TRP B 192 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG B 193 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 226 through 229 removed outlier: 5.807A pdb=" N LEU B 241 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 235 removed outlier: 6.664A pdb=" N LEU B 235 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN B 320 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET B 317 " --> pdb=" O LEU B 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 268 Processing sheet with id=AB1, first strand: chain 'B' and resid 326 through 330 removed outlier: 4.059A pdb=" N VAL B 341 " --> pdb=" O MET B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 334 through 336 Processing sheet with id=AB3, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB4, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.525A pdb=" N MET D 117 " --> pdb=" O TRP D 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU D 57 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 57 through 62 removed outlier: 3.613A pdb=" N GLU D 57 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 125 through 129 Processing sheet with id=AB8, first strand: chain 'D' and resid 133 through 135 removed outlier: 4.213A pdb=" N TRP D 192 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG D 193 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 226 through 229 removed outlier: 5.807A pdb=" N LEU D 241 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.664A pdb=" N LEU D 235 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN D 320 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET D 317 " --> pdb=" O LEU D 407 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 265 through 268 Processing sheet with id=AC3, first strand: chain 'D' and resid 326 through 330 removed outlier: 4.059A pdb=" N VAL D 341 " --> pdb=" O MET D 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 334 through 336 439 hydrogen bonds defined for protein. 1167 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: 2.62 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1926 1.33 - 1.45: 1864 1.45 - 1.57: 4692 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8550 Sorted by residual: bond pdb=" C HIS D 363 " pdb=" N PRO D 364 " ideal model delta sigma weight residual 1.331 1.368 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" C HIS B 363 " pdb=" N PRO B 364 " ideal model delta sigma weight residual 1.331 1.368 -0.037 8.70e-03 1.32e+04 1.81e+01 bond pdb=" C GLY D 284 " pdb=" N PRO D 285 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 9.90e+00 bond pdb=" C GLY B 284 " pdb=" N PRO B 285 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 9.90e+00 bond pdb=" C PHE B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.335 1.360 -0.025 8.70e-03 1.32e+04 8.46e+00 ... (remaining 8545 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.97: 382 106.97 - 114.13: 4586 114.13 - 121.30: 4788 121.30 - 128.46: 1728 128.46 - 135.63: 114 Bond angle restraints: 11598 Sorted by residual: angle pdb=" C GLU B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.76 113.46 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" C GLU D 67 " pdb=" N PRO D 68 " pdb=" CA PRO D 68 " ideal model delta sigma weight residual 119.76 113.46 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" C ARG D 267 " pdb=" N PRO D 268 " pdb=" CA PRO D 268 " ideal model delta sigma weight residual 120.03 114.22 5.81 9.90e-01 1.02e+00 3.45e+01 angle pdb=" C ARG B 267 " pdb=" N PRO B 268 " pdb=" CA PRO B 268 " ideal model delta sigma weight residual 120.03 114.22 5.81 9.90e-01 1.02e+00 3.45e+01 angle pdb=" C GLY D 184 " pdb=" N PRO D 185 " pdb=" CA PRO D 185 " ideal model delta sigma weight residual 119.84 126.74 -6.90 1.25e+00 6.40e-01 3.05e+01 ... (remaining 11593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.18: 4966 25.18 - 50.36: 152 50.36 - 75.54: 18 75.54 - 100.72: 2 100.72 - 125.90: 4 Dihedral angle restraints: 5142 sinusoidal: 2098 harmonic: 3044 Sorted by residual: dihedral pdb=" CA GLN B 330 " pdb=" C GLN B 330 " pdb=" N PRO B 331 " pdb=" CA PRO B 331 " ideal model delta harmonic sigma weight residual 180.00 54.10 125.90 0 5.00e+00 4.00e-02 6.34e+02 dihedral pdb=" CA GLN D 330 " pdb=" C GLN D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta harmonic sigma weight residual 180.00 54.10 125.90 0 5.00e+00 4.00e-02 6.34e+02 dihedral pdb=" CA GLY B 184 " pdb=" C GLY B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta harmonic sigma weight residual -180.00 -67.33 -112.67 0 5.00e+00 4.00e-02 5.08e+02 ... (remaining 5139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 758 0.040 - 0.080: 302 0.080 - 0.120: 116 0.120 - 0.159: 38 0.159 - 0.199: 2 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA SER A 54 " pdb=" N SER A 54 " pdb=" C SER A 54 " pdb=" CB SER A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA SER C 54 " pdb=" N SER C 54 " pdb=" C SER C 54 " pdb=" CB SER C 54 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CG LEU D 235 " pdb=" CB LEU D 235 " pdb=" CD1 LEU D 235 " pdb=" CD2 LEU D 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1213 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 131 " 0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO D 132 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 131 " -0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO B 132 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 86 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ALA A 86 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA A 86 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU A 87 " -0.009 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 2944 2.88 - 3.38: 7335 3.38 - 3.89: 14411 3.89 - 4.39: 16410 4.39 - 4.90: 26746 Nonbonded interactions: 67846 Sorted by model distance: nonbonded pdb=" OG SER D 102 " pdb=" O GLY D 105 " model vdw 2.373 2.440 nonbonded pdb=" OG SER B 102 " pdb=" O GLY B 105 " model vdw 2.373 2.440 nonbonded pdb=" NE ARG B 253 " pdb=" O HIS B 300 " model vdw 2.522 2.520 nonbonded pdb=" NE ARG D 253 " pdb=" O HIS D 300 " model vdw 2.522 2.520 nonbonded pdb=" O ARG B 223 " pdb=" OH TYR B 251 " model vdw 2.551 2.440 ... (remaining 67841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.100 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: 4.000 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 25.610 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 0.040 8550 Z= 0.429 Angle : 1.264 10.628 11598 Z= 0.795 Chirality : 0.051 0.199 1216 Planarity : 0.005 0.057 1514 Dihedral : 12.300 125.903 3170 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.46 % Favored : 96.15 % Rotamer: Outliers : 0.22 % Allowed : 5.83 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 8.11 % 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: -0.43 (0.25), residues: 1040 helix: 1.26 (0.28), residues: 256 sheet: -0.08 (0.28), residues: 310 loop : -1.28 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 26 HIS 0.003 0.001 HIS D 209 PHE 0.010 0.002 PHE B 177 TYR 0.020 0.002 TYR B 197 ARG 0.005 0.001 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 1.3430 time to fit residues: 218.4715 Evaluate side-chains 98 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 58 GLN A 81 GLN A 117 GLN A 128 GLN A 140 HIS A 156 GLN B 92 HIS B 190 HIS B 205 GLN B 280 ASN B 290 HIS B 301 ASN B 346 GLN C 46 GLN C 58 GLN C 81 GLN C 117 GLN C 128 GLN C 140 HIS C 156 GLN D 92 HIS D 190 HIS D 205 GLN D 290 HIS D 301 ASN D 346 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8550 Z= 0.227 Angle : 0.568 7.191 11598 Z= 0.297 Chirality : 0.039 0.145 1216 Planarity : 0.006 0.092 1514 Dihedral : 5.602 89.213 1164 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.58 % Favored : 99.23 % Rotamer: Outliers : 2.24 % Allowed : 10.31 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 5.41 % 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: 1.33 (0.27), residues: 1040 helix: 3.58 (0.29), residues: 254 sheet: 0.35 (0.28), residues: 318 loop : -0.24 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 32 HIS 0.004 0.001 HIS D 92 PHE 0.009 0.001 PHE D 351 TYR 0.017 0.002 TYR B 372 ARG 0.004 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7614 (ptm) REVERT: A 125 MET cc_start: 0.7648 (mmm) cc_final: 0.7339 (mmt) REVERT: A 151 ASP cc_start: 0.8153 (m-30) cc_final: 0.7889 (m-30) REVERT: B 32 TRP cc_start: 0.7318 (p90) cc_final: 0.6743 (p90) REVERT: C 64 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7613 (ptm) REVERT: C 125 MET cc_start: 0.7651 (mmm) cc_final: 0.7337 (mmt) REVERT: C 151 ASP cc_start: 0.8154 (m-30) cc_final: 0.7888 (m-30) REVERT: D 32 TRP cc_start: 0.7316 (p90) cc_final: 0.6741 (p90) outliers start: 20 outliers final: 6 residues processed: 114 average time/residue: 1.2825 time to fit residues: 155.1404 Evaluate side-chains 100 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 323 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN D 280 ASN ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8550 Z= 0.262 Angle : 0.545 6.705 11598 Z= 0.284 Chirality : 0.038 0.135 1216 Planarity : 0.006 0.099 1514 Dihedral : 5.150 81.601 1164 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % Rotamer: Outliers : 2.47 % Allowed : 11.66 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.62 (0.27), residues: 1040 helix: 3.77 (0.29), residues: 254 sheet: 0.58 (0.29), residues: 322 loop : -0.07 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 26 HIS 0.002 0.001 HIS A 140 PHE 0.007 0.001 PHE D 351 TYR 0.013 0.002 TYR D 197 ARG 0.002 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.8183 (m-30) cc_final: 0.7845 (m-30) REVERT: B 32 TRP cc_start: 0.7241 (p90) cc_final: 0.6711 (p90) REVERT: C 151 ASP cc_start: 0.8183 (m-30) cc_final: 0.7844 (m-30) REVERT: D 32 TRP cc_start: 0.7243 (p90) cc_final: 0.6711 (p90) outliers start: 22 outliers final: 14 residues processed: 118 average time/residue: 1.2006 time to fit residues: 151.0727 Evaluate side-chains 108 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 363 HIS B 405 HIS C 46 GLN D 363 HIS D 405 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8550 Z= 0.275 Angle : 0.530 6.471 11598 Z= 0.274 Chirality : 0.038 0.140 1216 Planarity : 0.006 0.098 1514 Dihedral : 5.096 77.955 1164 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.54 % Favored : 98.27 % Rotamer: Outliers : 3.59 % Allowed : 11.43 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.67 (0.27), residues: 1040 helix: 3.62 (0.29), residues: 254 sheet: 0.66 (0.28), residues: 324 loop : 0.05 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 26 HIS 0.004 0.001 HIS D 363 PHE 0.006 0.001 PHE B 351 TYR 0.012 0.002 TYR D 197 ARG 0.004 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7658 (ptm) REVERT: A 132 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7558 (tp30) REVERT: A 147 ARG cc_start: 0.8285 (mtt180) cc_final: 0.8058 (mtp180) REVERT: B 32 TRP cc_start: 0.7241 (p90) cc_final: 0.6887 (p90) REVERT: B 147 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: C 64 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7622 (ptm) REVERT: C 132 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: C 147 ARG cc_start: 0.8305 (mtt180) cc_final: 0.8082 (mtp180) REVERT: D 32 TRP cc_start: 0.7242 (p90) cc_final: 0.6900 (p90) REVERT: D 147 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7531 (mp10) outliers start: 32 outliers final: 14 residues processed: 126 average time/residue: 1.2271 time to fit residues: 164.3832 Evaluate side-chains 115 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 363 HIS C 46 GLN C 58 GLN D 363 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8550 Z= 0.234 Angle : 0.507 6.681 11598 Z= 0.261 Chirality : 0.037 0.135 1216 Planarity : 0.006 0.107 1514 Dihedral : 4.948 74.967 1164 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.31 % Favored : 97.50 % Rotamer: Outliers : 3.14 % Allowed : 13.23 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.65 (0.27), residues: 1040 helix: 3.60 (0.29), residues: 254 sheet: 0.56 (0.28), residues: 336 loop : 0.10 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 26 HIS 0.005 0.001 HIS D 363 PHE 0.004 0.001 PHE D 381 TYR 0.012 0.001 TYR D 197 ARG 0.004 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6499 (mt-10) REVERT: A 132 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: A 147 ARG cc_start: 0.8266 (mtt180) cc_final: 0.8032 (mtp85) REVERT: B 32 TRP cc_start: 0.7272 (p90) cc_final: 0.6906 (p90) REVERT: C 49 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6497 (mt-10) REVERT: C 64 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7697 (ptm) REVERT: C 132 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7560 (tp30) REVERT: C 147 ARG cc_start: 0.8264 (mtt180) cc_final: 0.8027 (mtp85) REVERT: D 32 TRP cc_start: 0.7276 (p90) cc_final: 0.6918 (p90) outliers start: 28 outliers final: 15 residues processed: 112 average time/residue: 1.1250 time to fit residues: 134.9132 Evaluate side-chains 108 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.0270 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 58 GLN B 363 HIS C 46 GLN D 363 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8550 Z= 0.188 Angle : 0.490 6.488 11598 Z= 0.251 Chirality : 0.037 0.133 1216 Planarity : 0.006 0.115 1514 Dihedral : 4.845 72.918 1164 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.69 % Allowed : 14.91 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.81 (0.27), residues: 1040 helix: 3.71 (0.29), residues: 254 sheet: 0.65 (0.28), residues: 340 loop : 0.23 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 26 HIS 0.005 0.001 HIS D 363 PHE 0.003 0.001 PHE D 281 TYR 0.011 0.001 TYR B 377 ARG 0.005 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7588 (ptm) REVERT: A 132 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: B 32 TRP cc_start: 0.7250 (p90) cc_final: 0.6892 (p90) REVERT: C 64 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7668 (ptm) REVERT: C 132 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: D 32 TRP cc_start: 0.7250 (p90) cc_final: 0.6898 (p90) outliers start: 24 outliers final: 12 residues processed: 101 average time/residue: 1.1548 time to fit residues: 124.9001 Evaluate side-chains 98 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 371 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 314 ASN B 363 HIS C 46 GLN D 363 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8550 Z= 0.193 Angle : 0.483 6.019 11598 Z= 0.249 Chirality : 0.036 0.135 1216 Planarity : 0.006 0.110 1514 Dihedral : 4.745 69.918 1164 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.24 % Allowed : 15.81 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.91 (0.27), residues: 1040 helix: 3.74 (0.29), residues: 254 sheet: 0.70 (0.28), residues: 340 loop : 0.33 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 26 HIS 0.005 0.001 HIS B 363 PHE 0.003 0.001 PHE C 33 TYR 0.011 0.001 TYR D 197 ARG 0.005 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7639 (ptm) REVERT: A 112 ARG cc_start: 0.7043 (mtm110) cc_final: 0.6840 (mtp85) REVERT: A 132 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: B 32 TRP cc_start: 0.7312 (p90) cc_final: 0.6995 (p90) REVERT: C 64 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7707 (ptm) REVERT: C 132 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: D 32 TRP cc_start: 0.7308 (p90) cc_final: 0.7001 (p90) REVERT: D 383 MET cc_start: 0.8147 (mtm) cc_final: 0.7944 (mtt) outliers start: 20 outliers final: 14 residues processed: 96 average time/residue: 1.1386 time to fit residues: 117.3555 Evaluate side-chains 96 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 371 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 363 HIS C 46 GLN D 314 ASN D 363 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8550 Z= 0.207 Angle : 0.483 5.817 11598 Z= 0.249 Chirality : 0.037 0.145 1216 Planarity : 0.005 0.105 1514 Dihedral : 4.767 69.951 1164 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.58 % Allowed : 15.13 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 1.96 (0.27), residues: 1040 helix: 3.71 (0.28), residues: 254 sheet: 0.74 (0.28), residues: 340 loop : 0.39 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 26 HIS 0.005 0.001 HIS D 363 PHE 0.004 0.001 PHE D 381 TYR 0.011 0.001 TYR D 197 ARG 0.004 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2080 Ramachandran restraints generated. 1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6533 (mt-10) REVERT: A 64 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7747 (ptm) REVERT: A 132 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: B 32 TRP cc_start: 0.7333 (p90) cc_final: 0.7042 (p90) REVERT: C 49 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6540 (mt-10) REVERT: C 64 MET cc_start: 0.8485 (ptt) cc_final: 0.7721 (ptm) REVERT: C 132 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: D 32 TRP cc_start: 0.7334 (p90) cc_final: 0.7044 (p90) outliers start: 23 outliers final: 15 residues processed: 96 average time/residue: 1.1769 time to fit residues: 121.2721 Evaluate side-chains 99 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 248 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 70.6279 > 50: distance: 37 - 187: 31.492 distance: 40 - 199: 25.454 distance: 102 - 162: 30.518 distance: 105 - 159: 32.196 distance: 133 - 138: 28.650 distance: 138 - 139: 35.346 distance: 139 - 140: 28.501 distance: 139 - 142: 11.340 distance: 142 - 143: 24.111 distance: 144 - 145: 56.367 distance: 145 - 146: 3.296 distance: 145 - 148: 39.796 distance: 146 - 147: 53.695 distance: 148 - 149: 16.899 distance: 149 - 150: 20.873 distance: 149 - 151: 22.176 distance: 152 - 153: 17.015 distance: 152 - 158: 38.071 distance: 153 - 154: 6.161 distance: 153 - 156: 20.492 distance: 154 - 155: 11.559 distance: 154 - 159: 11.552 distance: 159 - 160: 13.803 distance: 160 - 161: 31.788 distance: 160 - 163: 22.361 distance: 161 - 162: 25.833 distance: 161 - 167: 8.060 distance: 163 - 164: 9.851 distance: 164 - 165: 35.272 distance: 164 - 166: 14.279 distance: 167 - 168: 40.461 distance: 168 - 169: 3.569 distance: 168 - 171: 33.277 distance: 169 - 170: 19.044 distance: 169 - 176: 31.976 distance: 171 - 172: 27.620 distance: 172 - 173: 15.965 distance: 173 - 174: 34.877 distance: 173 - 175: 10.704 distance: 176 - 177: 14.387 distance: 177 - 178: 24.347 distance: 177 - 180: 16.122 distance: 178 - 179: 34.350 distance: 178 - 184: 48.393 distance: 184 - 185: 41.888 distance: 185 - 188: 17.840 distance: 186 - 187: 39.084 distance: 186 - 191: 29.650 distance: 188 - 189: 19.314 distance: 188 - 190: 46.108 distance: 191 - 192: 40.642 distance: 192 - 193: 30.538 distance: 192 - 195: 31.091 distance: 193 - 194: 41.098 distance: 193 - 199: 17.432 distance: 195 - 196: 40.302 distance: 196 - 197: 41.388 distance: 199 - 200: 16.842 distance: 200 - 203: 40.018 distance: 201 - 206: 39.637 distance: 203 - 205: 39.996 distance: 206 - 207: 4.083 distance: 207 - 208: 13.140 distance: 208 - 209: 43.972 distance: 208 - 210: 28.917