Starting phenix.real_space_refine on Fri Jul 19 09:41:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/07_2024/8h86_34530.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/07_2024/8h86_34530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/07_2024/8h86_34530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/07_2024/8h86_34530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/07_2024/8h86_34530.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/07_2024/8h86_34530.cif" } resolution = 2.56 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= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 60 5.16 5 C 4896 2.51 5 N 957 2.21 5 O 1158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 252": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7080 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2090 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2071 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2071 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2129 Chain: "A" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 270 Unusual residues: {'PLM': 5, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 16, 'water': 21} Link IDs: {None: 36} Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 6, 'PSC:plan-2': 6, 'PSC:plan-3': 6, 'PSC:plan-4': 6, 'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 2090 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2071 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2071 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2129 Chain: "B" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 270 Unusual residues: {'PLM': 5, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 16, 'water': 21} Link IDs: {None: 36} Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 6, 'PSC:plan-2': 6, 'PSC:plan-3': 6, 'PSC:plan-4': 6, 'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 2090 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2071 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2071 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2129 Chain: "C" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 270 Unusual residues: {'PLM': 5, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 16, 'water': 21} Link IDs: {None: 36} Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 6, 'PSC:plan-2': 6, 'PSC:plan-3': 6, 'PSC:plan-4': 6, 'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 105 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N APHE A 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 144 " occ=0.50 residue: pdb=" N APHE B 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 144 " occ=0.50 residue: pdb=" N APHE C 144 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 144 " occ=0.50 Time building chain proxies: 7.02, per 1000 atoms: 0.99 Number of scatterers: 7080 At special positions: 0 Unit cell: (78.02, 76.36, 82.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 9 15.00 O 1158 8.00 N 957 7.00 C 4896 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 2.2 seconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1422 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 21 through 49 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 103 through 122 removed outlier: 3.992A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.802A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 4.003A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.663A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 252 removed outlier: 3.633A pdb=" N ILE A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE A 236 " --> pdb=" O CYS A 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 49 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 103 through 122 removed outlier: 3.992A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.802A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.003A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.663A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 252 removed outlier: 3.634A pdb=" N ILE B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE B 236 " --> pdb=" O CYS B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 49 Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 103 through 122 removed outlier: 3.992A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.802A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 4.003A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.663A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 252 removed outlier: 3.633A pdb=" N ILE C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE C 236 " --> pdb=" O CYS C 232 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1305 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: 1.93 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1031 1.32 - 1.45: 2428 1.45 - 1.58: 3672 1.58 - 1.71: 15 1.71 - 1.84: 81 Bond restraints: 7227 Sorted by residual: bond pdb=" C7 PSC A 311 " pdb=" C8 PSC A 311 " ideal model delta sigma weight residual 1.530 1.322 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C7 PSC C 311 " pdb=" C8 PSC C 311 " ideal model delta sigma weight residual 1.530 1.322 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C7 PSC B 311 " pdb=" C8 PSC B 311 " ideal model delta sigma weight residual 1.530 1.323 0.207 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C6 PSC A 313 " pdb=" C7 PSC A 313 " ideal model delta sigma weight residual 1.523 1.319 0.204 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C6 PSC C 313 " pdb=" C7 PSC C 313 " ideal model delta sigma weight residual 1.523 1.319 0.204 2.00e-02 2.50e+03 1.05e+02 ... (remaining 7222 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.36: 273 106.36 - 113.38: 3374 113.38 - 120.41: 3394 120.41 - 127.44: 2496 127.44 - 134.47: 96 Bond angle restraints: 9633 Sorted by residual: angle pdb=" C10 PSC C 311 " pdb=" C11 PSC C 311 " pdb=" C12 PSC C 311 " ideal model delta sigma weight residual 111.07 125.84 -14.77 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C10 PSC A 311 " pdb=" C11 PSC A 311 " pdb=" C12 PSC A 311 " ideal model delta sigma weight residual 111.07 125.82 -14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C10 PSC B 311 " pdb=" C11 PSC B 311 " pdb=" C12 PSC B 311 " ideal model delta sigma weight residual 111.07 125.82 -14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C2 PSC B 312 " pdb=" C3 PSC B 312 " pdb=" C4 PSC B 312 " ideal model delta sigma weight residual 111.73 125.94 -14.21 3.00e+00 1.11e-01 2.24e+01 angle pdb=" C2 PSC C 312 " pdb=" C3 PSC C 312 " pdb=" C4 PSC C 312 " ideal model delta sigma weight residual 111.73 125.93 -14.20 3.00e+00 1.11e-01 2.24e+01 ... (remaining 9628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.23: 3785 25.23 - 50.45: 322 50.45 - 75.68: 66 75.68 - 100.90: 0 100.90 - 126.12: 6 Dihedral angle restraints: 4179 sinusoidal: 1938 harmonic: 2241 Sorted by residual: dihedral pdb=" C02 PSC C 303 " pdb=" C03 PSC C 303 " pdb=" O11 PSC C 303 " pdb=" P PSC C 303 " ideal model delta sinusoidal sigma weight residual 180.62 54.50 126.12 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C02 PSC B 303 " pdb=" C03 PSC B 303 " pdb=" O11 PSC B 303 " pdb=" P PSC B 303 " ideal model delta sinusoidal sigma weight residual 180.62 54.51 126.11 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C02 PSC A 303 " pdb=" C03 PSC A 303 " pdb=" O11 PSC A 303 " pdb=" P PSC A 303 " ideal model delta sinusoidal sigma weight residual 180.62 54.54 126.08 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 4176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 458 0.052 - 0.105: 299 0.105 - 0.157: 109 0.157 - 0.209: 58 0.209 - 0.261: 9 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA TYR B 81 " pdb=" N TYR B 81 " pdb=" C TYR B 81 " pdb=" CB TYR B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA TYR C 81 " pdb=" N TYR C 81 " pdb=" C TYR C 81 " pdb=" CB TYR C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA TYR A 81 " pdb=" N TYR A 81 " pdb=" C TYR A 81 " pdb=" CB TYR A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 930 not shown) Planarity restraints: 1155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 PSC B 311 " 0.268 2.00e-02 2.50e+03 2.81e-01 7.87e+02 pdb=" C12 PSC B 311 " -0.238 2.00e-02 2.50e+03 pdb=" C13 PSC B 311 " -0.320 2.00e-02 2.50e+03 pdb=" C14 PSC B 311 " 0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PSC C 311 " -0.268 2.00e-02 2.50e+03 2.80e-01 7.87e+02 pdb=" C12 PSC C 311 " 0.238 2.00e-02 2.50e+03 pdb=" C13 PSC C 311 " 0.320 2.00e-02 2.50e+03 pdb=" C14 PSC C 311 " -0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PSC A 311 " -0.268 2.00e-02 2.50e+03 2.80e-01 7.86e+02 pdb=" C12 PSC A 311 " 0.238 2.00e-02 2.50e+03 pdb=" C13 PSC A 311 " 0.320 2.00e-02 2.50e+03 pdb=" C14 PSC A 311 " -0.289 2.00e-02 2.50e+03 ... (remaining 1152 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1904 2.82 - 3.34: 6804 3.34 - 3.86: 12425 3.86 - 4.38: 15633 4.38 - 4.90: 25093 Nonbonded interactions: 61859 Sorted by model distance: nonbonded pdb=" OG SER A 68 " pdb=" O HOH A 401 " model vdw 2.296 2.440 nonbonded pdb=" OG SER C 68 " pdb=" O HOH C 401 " model vdw 2.296 2.440 nonbonded pdb=" OG SER B 68 " pdb=" O HOH B 401 " model vdw 2.296 2.440 nonbonded pdb=" OG1 THR A 146 " pdb=" O HOH A 402 " model vdw 2.385 2.440 nonbonded pdb=" NH2 ARG C 171 " pdb=" O13 PSC C 310 " model vdw 2.385 2.520 ... (remaining 61854 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' and (resid 6 through 143 or resid 145 through 226 or resid 228 throug \ h 260 or resid 301 through 316)) selection = (chain 'B' and (resid 6 through 143 or resid 145 through 226 or resid 228 throug \ h 260 or resid 301 through 316)) selection = (chain 'C' and (resid 6 through 143 or resid 145 through 226 or resid 228 throug \ h 260 or resid 301 through 316)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.880 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.014 0.208 7227 Z= 0.843 Angle : 1.563 14.769 9633 Z= 0.928 Chirality : 0.082 0.261 933 Planarity : 0.030 0.281 1155 Dihedral : 18.473 126.125 2757 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.45 % Allowed : 2.26 % Favored : 97.29 % 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: -0.67 (0.28), residues: 771 helix: -0.49 (0.18), residues: 537 sheet: None (None), residues: 0 loop : 0.15 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.009 TRP B 190 HIS 0.014 0.004 HIS A 172 PHE 0.047 0.010 PHE A 86 TYR 0.043 0.009 TYR C 155 ARG 0.027 0.003 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.698 Fit side-chains REVERT: A 20 MET cc_start: 0.7679 (mtm) cc_final: 0.7391 (mtm) REVERT: A 170 MET cc_start: 0.6515 (mtm) cc_final: 0.6266 (mtt) REVERT: B 60 SER cc_start: 0.7505 (m) cc_final: 0.7289 (t) REVERT: B 170 MET cc_start: 0.6548 (mtm) cc_final: 0.6181 (mtt) REVERT: B 186 ARG cc_start: 0.6295 (ttm170) cc_final: 0.5676 (ttt180) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 1.4169 time to fit residues: 143.9315 Evaluate side-chains 85 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.7836 > 50: distance: 67 - 79: 3.004 distance: 92 - 108: 5.821 distance: 96 - 114: 7.629 distance: 101 - 125: 3.511 distance: 104 - 108: 3.267 distance: 105 - 133: 16.020 distance: 109 - 110: 7.230 distance: 109 - 112: 12.130 distance: 110 - 111: 7.728 distance: 110 - 114: 6.721 distance: 111 - 144: 20.803 distance: 112 - 113: 38.493 distance: 114 - 115: 7.361 distance: 115 - 116: 5.582 distance: 115 - 118: 12.238 distance: 116 - 117: 3.834 distance: 116 - 125: 3.171 distance: 117 - 155: 16.874 distance: 118 - 119: 10.450 distance: 119 - 120: 10.217 distance: 119 - 121: 20.454 distance: 120 - 122: 7.377 distance: 121 - 123: 12.255 distance: 122 - 124: 8.029 distance: 123 - 124: 7.491 distance: 125 - 126: 5.368 distance: 126 - 127: 4.677 distance: 126 - 129: 6.665 distance: 127 - 128: 14.971 distance: 127 - 133: 19.617 distance: 129 - 130: 5.415 distance: 130 - 131: 11.073 distance: 130 - 132: 13.033 distance: 133 - 134: 18.345 distance: 134 - 135: 4.276 distance: 134 - 137: 10.020 distance: 135 - 136: 12.319 distance: 135 - 144: 17.697 distance: 137 - 138: 13.367 distance: 138 - 139: 11.565 distance: 138 - 140: 21.918 distance: 139 - 141: 20.711 distance: 140 - 142: 14.615 distance: 141 - 143: 14.556 distance: 142 - 143: 17.050 distance: 144 - 145: 10.448 distance: 145 - 146: 12.979 distance: 145 - 148: 35.973 distance: 146 - 147: 3.112 distance: 146 - 155: 29.715 distance: 148 - 149: 17.073 distance: 149 - 150: 10.751 distance: 149 - 151: 18.240 distance: 150 - 152: 25.054 distance: 151 - 153: 22.461 distance: 152 - 154: 22.357 distance: 153 - 154: 28.938 distance: 155 - 156: 10.617 distance: 156 - 157: 27.376 distance: 156 - 159: 12.730 distance: 157 - 158: 6.666 distance: 157 - 163: 29.922 distance: 159 - 160: 18.518 distance: 160 - 161: 30.353 distance: 160 - 162: 23.437 distance: 163 - 164: 25.328 distance: 164 - 165: 3.631 distance: 165 - 166: 15.894 distance: 165 - 167: 13.605 distance: 167 - 168: 8.053 distance: 168 - 169: 14.258 distance: 169 - 170: 17.999 distance: 169 - 171: 18.402 distance: 171 - 172: 19.716 distance: 172 - 173: 24.871 distance: 173 - 174: 20.205 distance: 173 - 175: 21.897 distance: 175 - 176: 12.578 distance: 176 - 177: 8.103 distance: 176 - 179: 11.231 distance: 177 - 178: 15.084 distance: 177 - 182: 10.613 distance: 179 - 180: 20.905 distance: 179 - 181: 13.204