Starting phenix.real_space_refine on Fri Jul 19 09:27:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/07_2024/8iu0_35713.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/07_2024/8iu0_35713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/07_2024/8iu0_35713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/07_2024/8iu0_35713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/07_2024/8iu0_35713.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iu0_35713/07_2024/8iu0_35713.cif" } resolution = 2.66 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= 0.004 sd= 0.125 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 4863 2.51 5 N 954 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ARG 186": "NH1" <-> "NH2" 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 7": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B ARG 186": "NH1" <-> "NH2" 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 7": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C ARG 186": "NH1" <-> "NH2" 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: 7062 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2117 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 252 Unusual residues: {'PLM': 4, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 15, 'water': 26} Link IDs: {None: 40} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 341 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': 7, 'PSC:plan-4': 7, 'PLM:plan-1': 4} Unresolved non-hydrogen planarities: 109 Chain: "B" Number of atoms: 2102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2117 Chain: "B" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 252 Unusual residues: {'PLM': 4, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 15, 'water': 26} Link IDs: {None: 40} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 341 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': 7, 'PSC:plan-4': 7, 'PLM:plan-1': 4} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 2102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 255, 2072 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 16, 'TRANS': 238} bond proxies already assigned to first conformer: 2117 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 252 Unusual residues: {'PLM': 4, 'PSC': 10, 'RET': 1} Classifications: {'undetermined': 15, 'water': 26} Link IDs: {None: 40} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 341 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': 7, 'PSC:plan-4': 7, 'PLM:plan-1': 4} Unresolved non-hydrogen planarities: 109 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N APHE A 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 35 " occ=0.50 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 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 35 " 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 35 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 35 " 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: 7.25, per 1000 atoms: 1.03 Number of scatterers: 7062 At special positions: 0 Unit cell: (77.19, 77.19, 84.66, 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 1176 8.00 N 954 7.00 C 4863 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: 3.14 Conformation dependent library (CDL) restraints added in 2.2 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 74.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR A 109 " --> pdb=" O ASP A 105 " (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: 3.781A 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: 4.122A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR B 109 " --> pdb=" O ASP B 105 " (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: 3.781A 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: 4.122A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 removed outlier: 3.644A pdb=" N THR C 109 " --> pdb=" O ASP C 105 " (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: 3.781A 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: 4.122A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.670A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 426 hydrogen bonds defined for protein. 1281 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: 1.69 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1226 1.33 - 1.46: 2621 1.46 - 1.59: 3260 1.59 - 1.72: 15 1.72 - 1.85: 81 Bond restraints: 7203 Sorted by residual: bond pdb=" C7 PSC C 310 " pdb=" C8 PSC C 310 " ideal model delta sigma weight residual 1.530 1.319 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC A 311 " pdb=" C4 PSC A 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC B 311 " pdb=" C4 PSC B 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C3 PSC C 311 " pdb=" C4 PSC C 311 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C7 PSC A 310 " pdb=" C8 PSC A 310 " ideal model delta sigma weight residual 1.530 1.320 0.210 2.00e-02 2.50e+03 1.11e+02 ... (remaining 7198 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.65: 293 106.65 - 113.63: 3414 113.63 - 120.61: 3523 120.61 - 127.60: 2310 127.60 - 134.58: 90 Bond angle restraints: 9630 Sorted by residual: angle pdb=" C10 PSC B 310 " pdb=" C9 PSC B 310 " pdb=" C8 PSC B 310 " ideal model delta sigma weight residual 127.68 112.60 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C10 PSC A 310 " pdb=" C9 PSC A 310 " pdb=" C8 PSC A 310 " ideal model delta sigma weight residual 127.68 112.60 15.08 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C10 PSC C 310 " pdb=" C9 PSC C 310 " pdb=" C8 PSC C 310 " ideal model delta sigma weight residual 127.68 112.61 15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C10 PSC B 310 " pdb=" C11 PSC B 310 " pdb=" C12 PSC B 310 " ideal model delta sigma weight residual 111.07 126.14 -15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C10 PSC A 310 " pdb=" C11 PSC A 310 " pdb=" C12 PSC A 310 " ideal model delta sigma weight residual 111.07 126.12 -15.05 3.00e+00 1.11e-01 2.52e+01 ... (remaining 9625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 3708 23.98 - 47.95: 324 47.95 - 71.93: 108 71.93 - 95.90: 0 95.90 - 119.88: 3 Dihedral angle restraints: 4143 sinusoidal: 1890 harmonic: 2253 Sorted by residual: dihedral pdb=" C03 PSC C 302 " pdb=" O11 PSC C 302 " pdb=" P PSC C 302 " pdb=" O12 PSC C 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.58 119.88 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C03 PSC A 302 " pdb=" O11 PSC A 302 " pdb=" P PSC A 302 " pdb=" O12 PSC A 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.59 119.87 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C03 PSC B 302 " pdb=" O11 PSC B 302 " pdb=" P PSC B 302 " pdb=" O12 PSC B 302 " ideal model delta sinusoidal sigma weight residual 174.46 54.60 119.86 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 457 0.051 - 0.102: 326 0.102 - 0.153: 113 0.153 - 0.204: 31 0.204 - 0.255: 9 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA PRO A 147 " pdb=" N PRO A 147 " pdb=" C PRO A 147 " pdb=" CB PRO A 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO C 147 " pdb=" N PRO C 147 " pdb=" C PRO C 147 " pdb=" CB PRO C 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO B 147 " pdb=" N PRO B 147 " pdb=" C PRO B 147 " pdb=" CB PRO B 147 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 933 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PSC B 312 " -0.310 2.00e-02 2.50e+03 2.30e-01 5.28e+02 pdb=" C11 PSC B 312 " 0.102 2.00e-02 2.50e+03 pdb=" C8 PSC B 312 " -0.100 2.00e-02 2.50e+03 pdb=" C9 PSC B 312 " 0.308 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC A 312 " -0.310 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C11 PSC A 312 " 0.102 2.00e-02 2.50e+03 pdb=" C8 PSC A 312 " -0.099 2.00e-02 2.50e+03 pdb=" C9 PSC A 312 " 0.307 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC C 312 " 0.310 2.00e-02 2.50e+03 2.30e-01 5.27e+02 pdb=" C11 PSC C 312 " -0.102 2.00e-02 2.50e+03 pdb=" C8 PSC C 312 " 0.099 2.00e-02 2.50e+03 pdb=" C9 PSC C 312 " -0.307 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1588 2.79 - 3.32: 6677 3.32 - 3.84: 12411 3.84 - 4.37: 15914 4.37 - 4.90: 25235 Nonbonded interactions: 61825 Sorted by model distance: nonbonded pdb=" OH TYR A 103 " pdb=" O HOH A 401 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR C 103 " pdb=" O HOH C 401 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR B 103 " pdb=" O HOH B 401 " model vdw 2.259 2.440 nonbonded pdb=" NH2 ARG C 171 " pdb=" O13 PSC C 309 " model vdw 2.306 2.520 nonbonded pdb=" NH2 ARG A 171 " pdb=" O13 PSC A 309 " model vdw 2.306 2.520 ... (remaining 61820 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 34 or resid 36 through 143 or resid 145 through \ 226 or resid 228 through 260 or resid 301 through 315)) selection = (chain 'B' and (resid 6 through 34 or resid 36 through 143 or resid 145 through \ 226 or resid 228 through 260 or resid 301 through 315)) selection = (chain 'C' and (resid 6 through 34 or resid 36 through 143 or resid 145 through \ 226 or resid 228 through 260 or resid 301 through 315)) } 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: 0.300 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.130 Find NCS groups from input model: 0.390 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:15.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 0.211 7203 Z= 0.870 Angle : 1.596 15.084 9630 Z= 0.937 Chirality : 0.077 0.255 936 Planarity : 0.023 0.230 1158 Dihedral : 18.616 119.879 2715 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.90 % Allowed : 4.95 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.27), residues: 780 helix: -1.30 (0.19), residues: 543 sheet: None (None), residues: 0 loop : -0.76 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.011 TRP B 187 HIS 0.011 0.006 HIS C 215 PHE 0.035 0.008 PHE B 243 TYR 0.044 0.009 TYR A 150 ARG 0.016 0.003 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.750 Fit side-chains REVERT: A 207 ILE cc_start: 0.7232 (mt) cc_final: 0.7024 (mm) REVERT: A 230 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6532 (tp) REVERT: B 207 ILE cc_start: 0.7118 (mt) cc_final: 0.6911 (mm) REVERT: C 207 ILE cc_start: 0.7298 (mt) cc_final: 0.7051 (mm) outliers start: 6 outliers final: 0 residues processed: 79 average time/residue: 1.3437 time to fit residues: 111.7173 Evaluate side-chains 63 residues out of total 648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU 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: 72.5277 > 50: distance: 34 - 39: 34.352 distance: 40 - 41: 41.405 distance: 40 - 43: 10.921 distance: 41 - 42: 12.455 distance: 41 - 47: 48.551 distance: 44 - 45: 33.981 distance: 44 - 46: 34.868 distance: 48 - 49: 38.848 distance: 49 - 50: 56.631 distance: 49 - 59: 41.059 distance: 50 - 84: 71.213 distance: 52 - 53: 69.023 distance: 52 - 54: 56.535 distance: 53 - 55: 56.056 distance: 55 - 57: 56.471 distance: 56 - 57: 40.481 distance: 57 - 58: 57.217 distance: 59 - 60: 38.666 distance: 60 - 61: 41.154 distance: 60 - 63: 56.616 distance: 61 - 62: 52.784 distance: 61 - 66: 39.628 distance: 63 - 64: 64.933 distance: 63 - 65: 57.518 distance: 67 - 68: 39.835 distance: 67 - 70: 58.300 distance: 68 - 69: 55.828 distance: 68 - 77: 41.265 distance: 70 - 71: 28.496 distance: 71 - 72: 34.595 distance: 71 - 73: 36.434 distance: 72 - 74: 55.726 distance: 74 - 76: 55.625 distance: 75 - 76: 46.654 distance: 77 - 78: 50.961 distance: 78 - 79: 32.888 distance: 78 - 81: 65.706 distance: 79 - 80: 39.193 distance: 81 - 82: 39.364 distance: 81 - 83: 57.694 distance: 84 - 85: 68.648 distance: 85 - 86: 41.239 distance: 86 - 87: 56.027 distance: 86 - 90: 39.619 distance: 87 - 113: 58.367 distance: 88 - 89: 55.101 distance: 90 - 91: 54.370 distance: 91 - 92: 39.859 distance: 91 - 94: 39.667 distance: 92 - 93: 54.273 distance: 92 - 97: 5.003 distance: 93 - 121: 35.415 distance: 94 - 95: 37.849 distance: 95 - 96: 56.165 distance: 97 - 98: 59.833 distance: 98 - 99: 8.275 distance: 98 - 101: 55.692 distance: 99 - 105: 34.052 distance: 100 - 129: 28.190 distance: 101 - 102: 15.526 distance: 102 - 103: 60.342 distance: 102 - 104: 19.177 distance: 105 - 106: 21.197 distance: 106 - 107: 55.706 distance: 106 - 109: 39.022 distance: 108 - 136: 32.844 distance: 109 - 110: 56.190 distance: 110 - 111: 40.902 distance: 110 - 112: 56.360 distance: 113 - 114: 19.247 distance: 114 - 115: 28.709 distance: 114 - 117: 6.418 distance: 115 - 116: 20.201 distance: 115 - 121: 21.385 distance: 116 - 143: 26.350 distance: 117 - 118: 43.170 distance: 117 - 119: 40.040 distance: 118 - 120: 39.593 distance: 155 - 167: 3.066