Starting phenix.real_space_refine on Sat Apr 6 04:50:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/04_2024/8h86_34530_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/04_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_34530/04_2024/8h86_34530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/04_2024/8h86_34530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/04_2024/8h86_34530_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h86_34530/04_2024/8h86_34530_updated.pdb" } 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-5288/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: 6.98, 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: 3.05 Conformation dependent library (CDL) restraints added in 2.3 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... running ksdssp... Secondary structure from input PDB file: 21 helices and 0 sheets defined 70.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 22 through 48 Processing helix chain 'A' and resid 65 through 89 removed outlier: 3.975A pdb=" N SER A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 71 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 89 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 121 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 126 through 145 Processing helix chain 'A' and resid 149 through 176 removed outlier: 4.259A pdb=" N THR A 163 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.741A pdb=" N LEU A 167 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 174 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 208 removed outlier: 4.003A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Proline residue: A 200 - end of helix Proline residue: A 203 - end of helix removed outlier: 3.663A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 251 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 22 through 48 Processing helix chain 'B' and resid 65 through 89 removed outlier: 3.975A pdb=" N SER B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 71 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 78 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 89 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 121 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 126 through 145 Processing helix chain 'B' and resid 149 through 176 removed outlier: 4.258A pdb=" N THR B 163 " --> pdb=" O CYS B 160 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 3.741A pdb=" N LEU B 167 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 174 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 208 removed outlier: 4.003A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Proline residue: B 200 - end of helix Proline residue: B 203 - end of helix removed outlier: 3.663A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 251 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 22 through 48 Processing helix chain 'C' and resid 65 through 89 removed outlier: 3.975A pdb=" N SER C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C 71 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY C 78 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 89 " --> pdb=" O PHE C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 121 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 126 through 145 Processing helix chain 'C' and resid 149 through 176 removed outlier: 4.259A pdb=" N THR C 163 " --> pdb=" O CYS C 160 " (cutoff:3.500A) Proline residue: C 164 - end of helix removed outlier: 3.741A pdb=" N LEU C 167 " --> pdb=" O PRO C 164 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 174 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 208 removed outlier: 4.003A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Proline residue: C 200 - end of helix Proline residue: C 203 - end of helix removed outlier: 3.663A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 251 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) 390 hydrogen bonds defined for protein. 837 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: 1.85 Time building geometry restraints manager: 3.24 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: 1032 1.32 - 1.45: 2427 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: 3395 120.41 - 127.44: 2495 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 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 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 54.54 126.08 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: 300 0.105 - 0.157: 108 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 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 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 1.64e+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: 1916 2.82 - 3.34: 6867 3.34 - 3.86: 12386 3.86 - 4.38: 15771 4.38 - 4.90: 25111 Nonbonded interactions: 62051 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 62046 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: 0.000 Extract box with map and model: 1.520 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 26.200 Find NCS groups from input model: 0.630 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.120 ------------------------------------------------------------------------------- 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= 0.852 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 : 0.768 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: 0.7504 (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: 1.5251 time to fit residues: 154.7339 Evaluate side-chains 85 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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: 69.153 > 50: distance: 82 - 102: 30.612 distance: 85 - 110: 37.140 distance: 89 - 117: 37.057 distance: 93 - 102: 31.192 distance: 94 - 125: 19.242 distance: 102 - 103: 16.608 distance: 103 - 104: 43.663 distance: 103 - 106: 26.865 distance: 104 - 105: 25.733 distance: 104 - 110: 57.688 distance: 105 - 139: 4.251 distance: 106 - 107: 35.502 distance: 107 - 108: 55.924 distance: 107 - 109: 56.098 distance: 111 - 112: 33.462 distance: 111 - 114: 40.030 distance: 112 - 113: 33.438 distance: 112 - 117: 5.697 distance: 113 - 145: 23.780 distance: 114 - 115: 56.830 distance: 118 - 119: 26.223 distance: 118 - 121: 17.445 distance: 119 - 120: 43.968 distance: 119 - 125: 38.966 distance: 120 - 149: 58.846 distance: 121 - 122: 54.655 distance: 122 - 123: 22.667 distance: 122 - 124: 9.473 distance: 125 - 126: 35.880 distance: 126 - 127: 12.863 distance: 126 - 129: 24.972 distance: 127 - 128: 22.456 distance: 127 - 139: 30.485 distance: 128 - 156: 23.404 distance: 129 - 130: 16.343 distance: 130 - 131: 16.300 distance: 130 - 132: 17.500 distance: 131 - 133: 24.904 distance: 132 - 134: 23.151 distance: 132 - 135: 30.805 distance: 133 - 134: 15.825 distance: 134 - 136: 15.738 distance: 135 - 137: 22.222 distance: 136 - 138: 18.190 distance: 137 - 138: 30.703 distance: 139 - 140: 28.181 distance: 140 - 141: 35.399 distance: 140 - 143: 25.827 distance: 141 - 142: 37.258 distance: 141 - 145: 30.968 distance: 142 - 161: 39.282 distance: 143 - 144: 33.736 distance: 145 - 146: 7.982 distance: 146 - 147: 42.819 distance: 147 - 148: 13.404 distance: 147 - 149: 25.886 distance: 148 - 166: 52.276 distance: 148 - 177: 46.656 distance: 149 - 150: 7.856 distance: 150 - 151: 21.992 distance: 150 - 153: 27.189 distance: 151 - 152: 19.822 distance: 151 - 156: 23.929 distance: 152 - 188: 27.728 distance: 153 - 154: 42.199 distance: 153 - 155: 29.491 distance: 156 - 157: 19.301 distance: 157 - 158: 14.139 distance: 157 - 160: 4.807 distance: 158 - 159: 13.477 distance: 158 - 161: 19.166 distance: 161 - 162: 16.590 distance: 162 - 163: 34.351 distance: 162 - 165: 35.503 distance: 163 - 164: 34.957 distance: 163 - 166: 56.744 distance: 163 - 177: 29.479 distance: 166 - 167: 27.643 distance: 167 - 168: 9.621 distance: 167 - 170: 37.459 distance: 168 - 169: 7.268 distance: 168 - 188: 21.997 distance: 170 - 171: 31.354 distance: 171 - 172: 9.038 distance: 171 - 173: 25.802 distance: 172 - 174: 14.179 distance: 173 - 175: 11.552 distance: 174 - 176: 26.295 distance: 175 - 176: 11.016 distance: 177 - 178: 11.317 distance: 178 - 179: 10.484 distance: 178 - 181: 24.755 distance: 179 - 180: 15.453 distance: 179 - 188: 21.515 distance: 181 - 182: 20.733 distance: 182 - 183: 12.375 distance: 182 - 184: 14.554 distance: 183 - 185: 8.067 distance: 184 - 186: 13.656 distance: 185 - 187: 5.093 distance: 186 - 187: 9.696