Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 03:01:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/08_2023/8gi9_40063_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/08_2023/8gi9_40063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/08_2023/8gi9_40063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/08_2023/8gi9_40063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/08_2023/8gi9_40063_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi9_40063/08_2023/8gi9_40063_updated.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.222 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 39 5.16 5 Na 9 4.78 5 C 4842 2.51 5 N 894 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 6852 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2284 Unusual residues: {' NA': 3, 'CLR': 7, 'PEE': 2, 'RET': 1} Classifications: {'peptide': 240, 'undetermined': 13, 'water': 15} Link IDs: {'PTRANS': 12, 'TRANS': 227, None: 28} Not linked: pdbres="LEU A 256 " pdbres="RET A 301 " Not linked: pdbres="RET A 301 " pdbres=" NA A 302 " Not linked: pdbres=" NA A 302 " pdbres=" NA A 303 " Not linked: pdbres=" NA A 303 " pdbres=" NA A 304 " Not linked: pdbres=" NA A 304 " pdbres="CLR A 305 " ... (remaining 23 not shown) Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2284 Unusual residues: {' NA': 3, 'CLR': 7, 'PEE': 2, 'RET': 1} Classifications: {'peptide': 240, 'undetermined': 13, 'water': 15} Link IDs: {'PTRANS': 12, 'TRANS': 227, None: 28} Not linked: pdbres="LEU B 256 " pdbres="RET B 301 " Not linked: pdbres="RET B 301 " pdbres=" NA B 302 " Not linked: pdbres=" NA B 302 " pdbres=" NA B 303 " Not linked: pdbres=" NA B 303 " pdbres=" NA B 304 " Not linked: pdbres=" NA B 304 " pdbres="CLR B 305 " ... (remaining 23 not shown) Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2284 Unusual residues: {' NA': 3, 'CLR': 7, 'PEE': 2, 'RET': 1} Classifications: {'peptide': 240, 'undetermined': 13, 'water': 15} Link IDs: {'PTRANS': 12, 'TRANS': 227, None: 28} Not linked: pdbres="LEU C 256 " pdbres="RET C 301 " Not linked: pdbres="RET C 301 " pdbres=" NA C 302 " Not linked: pdbres=" NA C 302 " pdbres=" NA C 303 " Not linked: pdbres=" NA C 303 " pdbres=" NA C 304 " Not linked: pdbres=" NA C 304 " pdbres="CLR C 305 " ... (remaining 23 not shown) Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.23, per 1000 atoms: 0.62 Number of scatterers: 6852 At special positions: 0 Unit cell: (79.31, 78.28, 76.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 6 15.00 Na 9 11.00 O 1062 8.00 N 894 7.00 C 4842 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: 3.22 Conformation dependent library (CDL) restraints added in 921.6 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 removed outlier: 3.562A pdb=" N ASP A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 89 removed outlier: 4.073A pdb=" N SER A 68 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 69 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 73 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 76 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 89 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.248A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 126 through 145 Processing helix chain 'A' and resid 149 through 176 removed outlier: 3.599A pdb=" N PHE A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 154 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL A 163 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.669A pdb=" N PHE A 167 " --> pdb=" O PRO A 164 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 169 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 208 removed outlier: 3.904A pdb=" N LEU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix Proline residue: A 203 - end of helix Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'B' and resid 22 through 49 removed outlier: 3.562A pdb=" N ASP B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 89 removed outlier: 4.074A pdb=" N SER B 68 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B 69 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 73 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 76 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 89 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.247A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 108' Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 126 through 145 Processing helix chain 'B' and resid 149 through 176 removed outlier: 3.599A pdb=" N PHE B 152 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B 154 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B 163 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 3.669A pdb=" N PHE B 167 " --> pdb=" O PRO B 164 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 169 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 208 removed outlier: 3.904A pdb=" N LEU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix Proline residue: B 203 - end of helix Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 234 through 251 Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.562A pdb=" N ASP C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 89 removed outlier: 4.074A pdb=" N SER C 68 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE C 69 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 73 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 76 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 89 " --> pdb=" O PHE C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.248A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 108' Processing helix chain 'C' and resid 110 through 121 Processing helix chain 'C' and resid 126 through 145 Processing helix chain 'C' and resid 149 through 176 removed outlier: 3.599A pdb=" N PHE C 152 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 154 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL C 163 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Proline residue: C 164 - end of helix removed outlier: 3.668A pdb=" N PHE C 167 " --> pdb=" O PRO C 164 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 169 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 208 removed outlier: 3.904A pdb=" N LEU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Proline residue: C 200 - end of helix Proline residue: C 203 - end of helix Processing helix chain 'C' and resid 218 through 232 Processing helix chain 'C' and resid 234 through 251 354 hydrogen bonds defined for protein. 765 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: 1.77 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1518 1.33 - 1.45: 1520 1.45 - 1.57: 3877 1.57 - 1.69: 114 1.69 - 1.81: 57 Bond restraints: 7086 Sorted by residual: bond pdb=" O4P PEE A 312 " pdb=" P PEE A 312 " ideal model delta sigma weight residual 1.653 1.786 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" O4P PEE B 312 " pdb=" P PEE B 312 " ideal model delta sigma weight residual 1.653 1.786 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O4P PEE C 312 " pdb=" P PEE C 312 " ideal model delta sigma weight residual 1.653 1.785 -0.132 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O4P PEE B 313 " pdb=" P PEE B 313 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" O4P PEE A 313 " pdb=" P PEE A 313 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 90.71 - 99.37: 18 99.37 - 108.03: 556 108.03 - 116.69: 4443 116.69 - 125.36: 4481 125.36 - 134.02: 207 Bond angle restraints: 9705 Sorted by residual: angle pdb=" O1P PEE B 312 " pdb=" P PEE B 312 " pdb=" O2P PEE B 312 " ideal model delta sigma weight residual 119.43 133.02 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE A 312 " pdb=" P PEE A 312 " pdb=" O2P PEE A 312 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE C 312 " pdb=" P PEE C 312 " pdb=" O2P PEE C 312 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE B 313 " pdb=" P PEE B 313 " pdb=" O2P PEE B 313 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE A 313 " pdb=" P PEE A 313 " pdb=" O2P PEE A 313 " ideal model delta sigma weight residual 119.43 133.00 -13.57 3.00e+00 1.11e-01 2.05e+01 ... (remaining 9700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 3618 29.20 - 58.39: 129 58.39 - 87.59: 15 87.59 - 116.78: 3 116.78 - 145.98: 3 Dihedral angle restraints: 3768 sinusoidal: 1686 harmonic: 2082 Sorted by residual: dihedral pdb=" C32 PEE A 312 " pdb=" C30 PEE A 312 " pdb=" C31 PEE A 312 " pdb=" O3 PEE A 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.86 -145.98 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C32 PEE C 312 " pdb=" C30 PEE C 312 " pdb=" C31 PEE C 312 " pdb=" O3 PEE C 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.87 -145.97 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C32 PEE B 312 " pdb=" C30 PEE B 312 " pdb=" C31 PEE B 312 " pdb=" O3 PEE B 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.89 -145.95 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 3765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 892 0.078 - 0.157: 74 0.157 - 0.235: 3 0.235 - 0.313: 54 0.313 - 0.391: 33 Chirality restraints: 1056 Sorted by residual: chirality pdb=" C2 PEE A 312 " pdb=" C1 PEE A 312 " pdb=" C3 PEE A 312 " pdb=" O2 PEE A 312 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C2 PEE C 312 " pdb=" C1 PEE C 312 " pdb=" C3 PEE C 312 " pdb=" O2 PEE C 312 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C17 CLR A 305 " pdb=" C13 CLR A 305 " pdb=" C16 CLR A 305 " pdb=" C20 CLR A 305 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 1053 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 94 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.24e-01 pdb=" N PRO A 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 94 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.18e-01 pdb=" N PRO C 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 94 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.12e-01 pdb=" N PRO B 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.013 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 39 2.48 - 3.09: 4922 3.09 - 3.69: 9947 3.69 - 4.30: 16879 4.30 - 4.90: 27846 Nonbonded interactions: 59633 Sorted by model distance: nonbonded pdb=" OH TYR B 62 " pdb=" OE1 GLN C 175 " model vdw 1.878 2.440 nonbonded pdb=" OH TYR A 62 " pdb=" OE1 GLN B 175 " model vdw 1.878 2.440 nonbonded pdb=" OE1 GLN A 175 " pdb=" OH TYR C 62 " model vdw 1.878 2.440 nonbonded pdb=" O ALA A 132 " pdb=" OG1 THR A 136 " model vdw 2.243 2.440 nonbonded pdb=" O ALA B 132 " pdb=" OG1 THR B 136 " model vdw 2.243 2.440 ... (remaining 59628 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 'B' selection = chain 'C' } 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: 0.980 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: 3.570 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.520 Find NCS groups from input model: 0.390 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.009 0.133 7086 Z= 0.540 Angle : 1.113 13.589 9705 Z= 0.394 Chirality : 0.100 0.391 1056 Planarity : 0.003 0.023 1035 Dihedral : 15.660 145.981 2442 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.00 % 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: 1.20 (0.33), residues: 714 helix: 1.73 (0.24), residues: 504 sheet: None (None), residues: 0 loop : -1.58 (0.42), residues: 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.713 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 1.2402 time to fit residues: 99.4789 Evaluate side-chains 68 residues out of total 612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9009 ------------------------------------------------------------------------------- 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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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: 71.4471 > 50: distance: 35 - 45: 3.299 distance: 44 - 58: 18.046 distance: 47 - 51: 8.397 distance: 48 - 64: 30.916 distance: 51 - 52: 11.479 distance: 52 - 53: 13.655 distance: 52 - 55: 13.590 distance: 53 - 54: 9.233 distance: 53 - 58: 46.386 distance: 54 - 68: 45.693 distance: 55 - 56: 20.495 distance: 55 - 57: 21.102 distance: 58 - 59: 21.474 distance: 59 - 60: 36.356 distance: 59 - 62: 27.132 distance: 60 - 61: 26.982 distance: 60 - 64: 4.578 distance: 61 - 75: 48.146 distance: 62 - 63: 36.613 distance: 64 - 65: 38.987 distance: 65 - 66: 36.870 distance: 66 - 67: 19.498 distance: 66 - 68: 24.359 distance: 67 - 83: 54.374 distance: 68 - 69: 10.551 distance: 69 - 70: 32.812 distance: 69 - 72: 15.325 distance: 70 - 71: 48.270 distance: 70 - 75: 50.914 distance: 71 - 95: 62.960 distance: 72 - 73: 19.059 distance: 72 - 74: 17.176 distance: 75 - 76: 36.996 distance: 76 - 77: 5.361 distance: 76 - 79: 12.835 distance: 77 - 78: 5.117 distance: 77 - 83: 15.087 distance: 78 - 100: 42.742 distance: 79 - 80: 29.034 distance: 79 - 81: 41.418 distance: 80 - 82: 68.888 distance: 83 - 84: 32.969 distance: 84 - 85: 45.604 distance: 84 - 87: 43.804 distance: 85 - 86: 18.644 distance: 85 - 95: 12.521 distance: 86 - 105: 26.626 distance: 87 - 88: 7.070 distance: 88 - 89: 20.045 distance: 88 - 90: 39.745 distance: 89 - 91: 34.633 distance: 90 - 92: 56.130 distance: 91 - 93: 22.148 distance: 92 - 93: 19.204 distance: 93 - 94: 39.829 distance: 95 - 96: 42.400 distance: 96 - 97: 10.104 distance: 96 - 99: 57.333 distance: 97 - 100: 55.299 distance: 98 - 114: 52.746 distance: 100 - 101: 11.146 distance: 101 - 102: 26.311 distance: 101 - 104: 47.100 distance: 102 - 103: 43.695 distance: 102 - 105: 27.467 distance: 103 - 121: 31.272 distance: 105 - 106: 28.849 distance: 106 - 107: 27.370 distance: 106 - 109: 58.412 distance: 107 - 108: 22.158 distance: 107 - 114: 15.812 distance: 108 - 132: 28.063 distance: 109 - 110: 25.156 distance: 110 - 111: 46.918 distance: 111 - 112: 16.535 distance: 112 - 113: 6.429 distance: 114 - 115: 43.431 distance: 115 - 116: 20.655 distance: 115 - 118: 46.078 distance: 116 - 117: 28.279 distance: 116 - 121: 27.558 distance: 117 - 139: 28.959 distance: 118 - 119: 32.894 distance: 118 - 120: 57.895