Starting phenix.real_space_refine on Fri Jan 19 23:59:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xku_22225/01_2024/6xku_22225_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xku_22225/01_2024/6xku_22225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xku_22225/01_2024/6xku_22225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xku_22225/01_2024/6xku_22225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xku_22225/01_2024/6xku_22225_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xku_22225/01_2024/6xku_22225_updated.pdb" } resolution = 4.2 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= 0.003 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 Fe 10 7.16 5 S 78 5.16 5 C 8578 2.51 5 N 2155 2.21 5 O 2258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 107": "OE1" <-> "OE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "R GLU 125": "OE1" <-> "OE2" Residue "R GLU 185": "OE1" <-> "OE2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "P ARG 85": "NH1" <-> "NH2" Residue "P ARG 125": "NH1" <-> "NH2" Residue "Q ARG 82": "NH1" <-> "NH2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q ASP 203": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13079 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1365 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "R" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1365 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "C" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1801 Classifications: {'peptide': 235} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "Q" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1794 Classifications: {'peptide': 235} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 933 SG CYS E 133 30.892 60.280 26.108 0.25105.87 S ATOM 1079 SG CYS E 153 31.686 57.930 23.427 0.25107.21 S ATOM 2298 SG CYS R 133 82.864 27.948 41.694 0.25105.87 S ATOM 2444 SG CYS R 153 83.981 31.374 41.102 0.25107.21 S Residues with excluded nonbonded symmetry interactions: 53 residue: pdb=" N MET E 129 " occ=0.25 ... (6 atoms not shown) pdb=" CE MET E 129 " occ=0.25 residue: pdb=" N GLY E 131 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 131 " occ=0.25 residue: pdb=" N VAL E 132 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 132 " occ=0.25 residue: pdb=" N CYS E 133 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 133 " occ=0.25 residue: pdb=" N THR E 134 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 THR E 134 " occ=0.25 residue: pdb=" N HIS E 135 " occ=0.25 ... (8 atoms not shown) pdb=" NE2 HIS E 135 " occ=0.25 residue: pdb=" N LEU E 136 " occ=0.25 ... (6 atoms not shown) pdb=" CD2 LEU E 136 " occ=0.25 residue: pdb=" N GLY E 137 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 137 " occ=0.25 residue: pdb=" N CYS E 138 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 138 " occ=0.25 residue: pdb=" N VAL E 139 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 139 " occ=0.25 residue: pdb=" N PRO E 140 " occ=0.25 ... (5 atoms not shown) pdb=" CD PRO E 140 " occ=0.25 residue: pdb=" N GLY E 142 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 142 " occ=0.25 ... (remaining 41 not shown) Time building chain proxies: 7.46, per 1000 atoms: 0.57 Number of scatterers: 13079 At special positions: 0 Unit cell: (114.24, 99.28, 110.16, 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) Fe 10 26.01 S 78 16.00 O 2258 8.00 N 2155 7.00 C 8578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 138 " - pdb=" SG CYS R 155 " distance=2.03 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.26 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 501 " pdb="FE2 FES E 501 " - pdb=" ND1 HIS E 135 " pdb="FE2 FES E 501 " - pdb=" ND1 HIS E 156 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 153 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 133 " pdb=" FES R 501 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 156 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 135 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 133 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 153 " Number of angles added : 6 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 6 sheets defined 45.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'E' and resid 12 through 35 Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 42 through 48 removed outlier: 3.857A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET E 47 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 48' Processing helix chain 'E' and resid 79 through 86 Processing helix chain 'E' and resid 110 through 113 No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'R' and resid 12 through 36 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 79 through 86 Processing helix chain 'R' and resid 110 through 113 No H-bonds generated for 'chain 'R' and resid 110 through 113' Processing helix chain 'C' and resid 15 through 20 removed outlier: 4.900A pdb=" N HIS C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 47 through 67 removed outlier: 3.975A pdb=" N MET C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 91 through 117 removed outlier: 3.757A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 147 Processing helix chain 'C' and resid 154 through 168 removed outlier: 4.862A pdb=" N PHE C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 188 through 198 Processing helix chain 'C' and resid 201 through 218 removed outlier: 3.587A pdb=" N PHE C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 269 Processing helix chain 'C' and resid 277 through 280 Processing helix chain 'C' and resid 299 through 307 Processing helix chain 'C' and resid 317 through 322 removed outlier: 4.557A pdb=" N THR C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 348 removed outlier: 3.849A pdb=" N MET C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 361 through 380 Processing helix chain 'C' and resid 389 through 414 removed outlier: 5.576A pdb=" N LEU C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Proline residue: C 409 - end of helix Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.572A pdb=" N GLU D 32 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 128 through 135 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 221 through 249 Processing helix chain 'P' and resid 15 through 20 removed outlier: 4.900A pdb=" N HIS P 20 " --> pdb=" O GLU P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 32 Processing helix chain 'P' and resid 47 through 67 removed outlier: 3.976A pdb=" N MET P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 85 Processing helix chain 'P' and resid 90 through 117 removed outlier: 3.754A pdb=" N SER P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 147 Processing helix chain 'P' and resid 154 through 168 removed outlier: 4.864A pdb=" N PHE P 166 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY P 167 " --> pdb=" O THR P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 181 Processing helix chain 'P' and resid 188 through 198 Processing helix chain 'P' and resid 201 through 218 removed outlier: 3.587A pdb=" N PHE P 216 " --> pdb=" O HIS P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 269 Processing helix chain 'P' and resid 277 through 280 Processing helix chain 'P' and resid 299 through 307 Processing helix chain 'P' and resid 317 through 322 removed outlier: 4.558A pdb=" N THR P 322 " --> pdb=" O VAL P 318 " (cutoff:3.500A) Processing helix chain 'P' and resid 328 through 348 removed outlier: 3.848A pdb=" N MET P 343 " --> pdb=" O ALA P 339 " (cutoff:3.500A) Proline residue: P 347 - end of helix Processing helix chain 'P' and resid 357 through 359 No H-bonds generated for 'chain 'P' and resid 357 through 359' Processing helix chain 'P' and resid 361 through 380 Processing helix chain 'P' and resid 389 through 414 removed outlier: 5.576A pdb=" N LEU P 408 " --> pdb=" O PHE P 404 " (cutoff:3.500A) Proline residue: P 409 - end of helix Processing helix chain 'Q' and resid 20 through 30 Processing helix chain 'Q' and resid 34 through 36 No H-bonds generated for 'chain 'Q' and resid 34 through 36' Processing helix chain 'Q' and resid 45 through 48 removed outlier: 3.560A pdb=" N LEU Q 48 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 45 through 48' Processing helix chain 'Q' and resid 58 through 66 Processing helix chain 'Q' and resid 128 through 135 Processing helix chain 'Q' and resid 202 through 217 Processing helix chain 'Q' and resid 221 through 249 Processing sheet with id= A, first strand: chain 'E' and resid 64 through 67 Processing sheet with id= B, first strand: chain 'E' and resid 180 through 182 removed outlier: 3.606A pdb=" N ALA E 181 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA R 181 " --> pdb=" O LYS R 189 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'R' and resid 64 through 67 Processing sheet with id= E, first strand: chain 'D' and resid 153 through 155 Processing sheet with id= F, first strand: chain 'Q' and resid 153 through 155 534 hydrogen bonds defined for protein. 1569 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: 5.50 Time building geometry restraints manager: 6.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 5785 1.41 - 1.61: 7562 1.61 - 1.80: 103 1.80 - 2.00: 31 2.00 - 2.20: 28 Bond restraints: 13509 Sorted by residual: bond pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC P 501 " pdb=" CBC HEC P 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C2D HEC C 501 " pdb=" C3D HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 13504 not shown) Histogram of bond angle deviations from ideal: 86.91 - 105.45: 398 105.45 - 124.00: 17358 124.00 - 142.54: 752 142.54 - 161.08: 0 161.08 - 179.62: 12 Bond angle restraints: 18520 Sorted by residual: angle pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " pdb="FE2 FES R 501 " ideal model delta sigma weight residual 75.66 89.12 -13.46 1.14e+00 7.69e-01 1.39e+02 angle pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " pdb="FE2 FES E 501 " ideal model delta sigma weight residual 75.66 89.08 -13.42 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES R 501 " pdb="FE2 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.93 13.40 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES E 501 " pdb="FE2 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.94 13.39 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES R 501 " pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.78 13.55 1.20e+00 6.94e-01 1.28e+02 ... (remaining 18515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6978 17.90 - 35.81: 534 35.81 - 53.71: 82 53.71 - 71.61: 10 71.61 - 89.52: 22 Dihedral angle restraints: 7626 sinusoidal: 2836 harmonic: 4790 Sorted by residual: dihedral pdb=" C2B HEC P 501 " pdb=" C3B HEC P 501 " pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.34 82.34 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.17 82.17 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2C HEC P 502 " pdb=" C3C HEC P 502 " pdb=" CAC HEC P 502 " pdb=" CBC HEC P 502 " ideal model delta sinusoidal sigma weight residual 60.00 -17.13 77.13 2 1.00e+01 1.00e-02 4.56e+01 ... (remaining 7623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1917 0.146 - 0.292: 40 0.292 - 0.438: 1 0.438 - 0.584: 10 0.584 - 0.729: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CG LEU Q 244 " pdb=" CB LEU Q 244 " pdb=" CD1 LEU Q 244 " pdb=" CD2 LEU Q 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CG LEU D 244 " pdb=" CB LEU D 244 " pdb=" CD1 LEU D 244 " pdb=" CD2 LEU D 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB THR Q 198 " pdb=" CA THR Q 198 " pdb=" OG1 THR Q 198 " pdb=" CG2 THR Q 198 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.86e+00 ... (remaining 1967 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q 501 " 0.010 2.00e-02 2.50e+03 4.12e-02 3.82e+01 pdb=" C2C HEC Q 501 " -0.109 2.00e-02 2.50e+03 pdb=" C3C HEC Q 501 " 0.042 2.00e-02 2.50e+03 pdb=" C4C HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CHC HEC Q 501 " 0.018 2.00e-02 2.50e+03 pdb=" CHD HEC Q 501 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC Q 501 " 0.031 2.00e-02 2.50e+03 pdb=" NC HEC Q 501 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 501 " -0.010 2.00e-02 2.50e+03 4.11e-02 3.81e+01 pdb=" C2C HEC D 501 " 0.109 2.00e-02 2.50e+03 pdb=" C3C HEC D 501 " -0.042 2.00e-02 2.50e+03 pdb=" C4C HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CHC HEC D 501 " -0.018 2.00e-02 2.50e+03 pdb=" CHD HEC D 501 " 0.007 2.00e-02 2.50e+03 pdb=" CMC HEC D 501 " -0.031 2.00e-02 2.50e+03 pdb=" NC HEC D 501 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 222 " -0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C ASN C 222 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN C 222 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN C 223 " -0.025 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 169 2.57 - 3.15: 11861 3.15 - 3.73: 19561 3.73 - 4.32: 27430 4.32 - 4.90: 45486 Nonbonded interactions: 104507 Sorted by model distance: nonbonded pdb=" O THR E 186 " pdb=" OG1 THR E 187 " model vdw 1.987 2.440 nonbonded pdb=" O THR R 186 " pdb=" OG1 THR R 187 " model vdw 1.987 2.440 nonbonded pdb=" OG SER P 120 " pdb=" ND2 ASN P 222 " model vdw 1.988 2.520 nonbonded pdb=" NH2 ARG P 306 " pdb=" O MET P 383 " model vdw 2.007 2.520 nonbonded pdb=" NH2 ARG C 306 " pdb=" O MET C 383 " model vdw 2.007 2.520 ... (remaining 104502 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 'C' selection = chain 'P' } ncs_group { reference = (chain 'D' and (resid 5 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 257 or resid 501)) selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } 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=0.25 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.430 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: 3.280 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 41.840 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.150 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 0.220 13509 Z= 0.641 Angle : 0.996 15.835 18520 Z= 0.622 Chirality : 0.069 0.729 1970 Planarity : 0.006 0.082 2327 Dihedral : 13.797 89.516 4564 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 16.47 % Favored : 83.17 % Rotamer: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.04 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.56 % 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: -4.29 (0.17), residues: 1658 helix: -1.64 (0.16), residues: 782 sheet: -3.48 (0.49), residues: 64 loop : -4.18 (0.18), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 296 HIS 0.010 0.001 HIS P 111 PHE 0.021 0.001 PHE C 104 TYR 0.010 0.001 TYR C 297 ARG 0.002 0.000 ARG R 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 553 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 ASP cc_start: 0.3644 (p0) cc_final: 0.3358 (t0) REVERT: E 37 GLN cc_start: 0.8527 (pp30) cc_final: 0.8304 (pp30) REVERT: E 102 ASN cc_start: 0.7091 (p0) cc_final: 0.6481 (p0) REVERT: E 167 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7610 (mtp85) REVERT: E 174 ASN cc_start: 0.5896 (p0) cc_final: 0.5194 (p0) REVERT: R 76 ARG cc_start: 0.6091 (tpt170) cc_final: 0.5598 (tpt-90) REVERT: C 39 LYS cc_start: 0.6276 (mttt) cc_final: 0.5490 (pttt) REVERT: C 70 THR cc_start: 0.8989 (m) cc_final: 0.8387 (p) REVERT: C 94 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.7875 (ttt-90) REVERT: C 110 ILE cc_start: 0.9314 (mt) cc_final: 0.8858 (mm) REVERT: C 139 MET cc_start: 0.8107 (ptm) cc_final: 0.7763 (ptp) REVERT: C 175 SER cc_start: 0.8596 (m) cc_final: 0.8347 (t) REVERT: C 296 TRP cc_start: 0.8221 (p-90) cc_final: 0.7885 (p-90) REVERT: C 299 LEU cc_start: 0.8509 (mt) cc_final: 0.8252 (mt) REVERT: C 302 TYR cc_start: 0.8342 (t80) cc_final: 0.8140 (t80) REVERT: C 374 PHE cc_start: 0.8692 (t80) cc_final: 0.8443 (t80) REVERT: D 210 SER cc_start: 0.9550 (m) cc_final: 0.9220 (t) REVERT: D 254 LYS cc_start: 0.6759 (mttm) cc_final: 0.6222 (tptt) REVERT: P 175 SER cc_start: 0.8368 (m) cc_final: 0.7896 (t) REVERT: Q 32 GLU cc_start: 0.6689 (mt-10) cc_final: 0.5868 (mt-10) REVERT: Q 103 MET cc_start: 0.8767 (tpp) cc_final: 0.8533 (mmm) REVERT: Q 134 TYR cc_start: 0.7640 (t80) cc_final: 0.7132 (t80) REVERT: Q 155 ASN cc_start: 0.5972 (t0) cc_final: 0.5419 (t0) REVERT: Q 188 VAL cc_start: 0.7600 (t) cc_final: 0.7003 (m) REVERT: Q 222 VAL cc_start: 0.7975 (m) cc_final: 0.7767 (p) REVERT: Q 229 LEU cc_start: 0.8754 (tp) cc_final: 0.8537 (tt) outliers start: 2 outliers final: 1 residues processed: 555 average time/residue: 0.2745 time to fit residues: 211.8964 Evaluate side-chains 268 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 150 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 ASN C 72 HIS C 217 HIS C 279 ASN C 291 HIS D 191 GLN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 HIS ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 282 GLN Q 177 HIS ** Q 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 204 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13509 Z= 0.226 Angle : 0.728 10.211 18520 Z= 0.353 Chirality : 0.045 0.180 1970 Planarity : 0.006 0.070 2327 Dihedral : 8.682 88.853 1858 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.22 % Favored : 88.72 % Rotamer: Outliers : 0.40 % Allowed : 4.80 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.30 (0.20), residues: 1658 helix: 0.11 (0.18), residues: 810 sheet: -2.34 (0.63), residues: 52 loop : -3.40 (0.19), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 126 HIS 0.005 0.001 HIS P 111 PHE 0.023 0.001 PHE P 401 TYR 0.024 0.002 TYR P 199 ARG 0.008 0.001 ARG R 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 390 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 70 LYS cc_start: 0.7671 (pttp) cc_final: 0.6547 (pttp) REVERT: E 122 ASN cc_start: 0.6901 (p0) cc_final: 0.6370 (t0) REVERT: R 35 ILE cc_start: 0.8878 (mm) cc_final: 0.8603 (mm) REVERT: C 39 LYS cc_start: 0.6777 (mttt) cc_final: 0.5476 (tttm) REVERT: C 70 THR cc_start: 0.8925 (m) cc_final: 0.8531 (p) REVERT: C 93 MET cc_start: 0.8510 (mmm) cc_final: 0.8217 (mmm) REVERT: C 175 SER cc_start: 0.8600 (m) cc_final: 0.8191 (t) REVERT: C 296 TRP cc_start: 0.8217 (p-90) cc_final: 0.7937 (p-90) REVERT: D 71 ILE cc_start: 0.7826 (tp) cc_final: 0.7610 (tt) REVERT: D 134 TYR cc_start: 0.8391 (t80) cc_final: 0.8140 (t80) REVERT: P 79 SER cc_start: 0.9262 (p) cc_final: 0.9021 (m) REVERT: P 84 MET cc_start: 0.8412 (mtp) cc_final: 0.8122 (mtp) REVERT: P 305 LEU cc_start: 0.8483 (mt) cc_final: 0.8246 (mt) REVERT: P 374 PHE cc_start: 0.8886 (t80) cc_final: 0.8631 (t80) REVERT: Q 28 GLN cc_start: 0.6825 (tp-100) cc_final: 0.6576 (tp-100) REVERT: Q 96 MET cc_start: 0.7602 (mmp) cc_final: 0.7259 (mmm) REVERT: Q 155 ASN cc_start: 0.5586 (t0) cc_final: 0.4877 (t0) REVERT: Q 222 VAL cc_start: 0.8235 (m) cc_final: 0.8013 (p) REVERT: Q 245 THR cc_start: 0.8725 (p) cc_final: 0.8457 (p) outliers start: 5 outliers final: 2 residues processed: 394 average time/residue: 0.2570 time to fit residues: 150.0074 Evaluate side-chains 247 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 245 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN C 279 ASN D 20 GLN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 282 GLN ** Q 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13509 Z= 0.244 Angle : 0.726 15.225 18520 Z= 0.338 Chirality : 0.044 0.158 1970 Planarity : 0.005 0.059 2327 Dihedral : 8.498 88.817 1858 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.36 % Favored : 87.58 % Rotamer: Outliers : 0.32 % Allowed : 3.04 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.57 (0.20), residues: 1658 helix: 0.69 (0.18), residues: 793 sheet: -1.26 (0.67), residues: 60 loop : -2.98 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 400 HIS 0.005 0.001 HIS E 156 PHE 0.024 0.002 PHE C 330 TYR 0.035 0.002 TYR C 109 ARG 0.005 0.001 ARG Q 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 339 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 LYS cc_start: 0.7038 (mttt) cc_final: 0.5510 (tttm) REVERT: C 70 THR cc_start: 0.8799 (m) cc_final: 0.8446 (p) REVERT: C 84 MET cc_start: 0.8966 (mmm) cc_final: 0.8703 (mmm) REVERT: C 93 MET cc_start: 0.8556 (mmm) cc_final: 0.8335 (mmm) REVERT: C 94 ARG cc_start: 0.8072 (ttt180) cc_final: 0.7666 (ttt180) REVERT: C 175 SER cc_start: 0.8323 (m) cc_final: 0.8071 (t) REVERT: C 296 TRP cc_start: 0.8452 (p-90) cc_final: 0.8175 (p-90) REVERT: C 372 LEU cc_start: 0.8959 (tp) cc_final: 0.8735 (tt) REVERT: D 27 PHE cc_start: 0.8109 (t80) cc_final: 0.7826 (t80) REVERT: P 374 PHE cc_start: 0.9001 (t80) cc_final: 0.8799 (t80) REVERT: Q 28 GLN cc_start: 0.6991 (tp-100) cc_final: 0.5804 (tp40) REVERT: Q 32 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6340 (mt-10) REVERT: Q 76 SER cc_start: 0.8306 (p) cc_final: 0.8061 (p) REVERT: Q 78 GLU cc_start: 0.6487 (mp0) cc_final: 0.6116 (mp0) REVERT: Q 96 MET cc_start: 0.7672 (mmp) cc_final: 0.7344 (mmm) REVERT: Q 100 LEU cc_start: 0.9099 (mt) cc_final: 0.8877 (mt) REVERT: Q 155 ASN cc_start: 0.6607 (t0) cc_final: 0.5688 (t0) REVERT: Q 214 MET cc_start: 0.7825 (tpp) cc_final: 0.7614 (tpt) REVERT: Q 218 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7667 (mt-10) outliers start: 4 outliers final: 2 residues processed: 341 average time/residue: 0.2400 time to fit residues: 118.5675 Evaluate side-chains 243 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 0.0980 chunk 151 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN C 68 HIS C 99 ASN D 159 GLN ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 284 ASN Q 204 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13509 Z= 0.208 Angle : 0.665 10.837 18520 Z= 0.322 Chirality : 0.043 0.202 1970 Planarity : 0.005 0.058 2327 Dihedral : 8.343 86.179 1858 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.49 % Favored : 89.38 % Rotamer: Outliers : 0.16 % Allowed : 2.40 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.11 (0.21), residues: 1658 helix: 0.98 (0.19), residues: 796 sheet: -0.92 (0.68), residues: 60 loop : -2.66 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 180 HIS 0.005 0.001 HIS C 291 PHE 0.015 0.001 PHE P 298 TYR 0.033 0.002 TYR P 199 ARG 0.006 0.001 ARG Q 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 342 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 LYS cc_start: 0.6956 (mttt) cc_final: 0.5644 (tttm) REVERT: C 46 ILE cc_start: 0.7967 (pt) cc_final: 0.7540 (mm) REVERT: C 70 THR cc_start: 0.8744 (m) cc_final: 0.8409 (p) REVERT: C 84 MET cc_start: 0.8908 (mmm) cc_final: 0.8593 (mmm) REVERT: C 93 MET cc_start: 0.8480 (mmm) cc_final: 0.8269 (mmm) REVERT: C 175 SER cc_start: 0.8491 (m) cc_final: 0.8248 (t) REVERT: C 199 TYR cc_start: 0.9145 (t80) cc_final: 0.8483 (t80) REVERT: C 229 VAL cc_start: 0.8240 (p) cc_final: 0.7949 (p) REVERT: C 296 TRP cc_start: 0.8328 (p-90) cc_final: 0.8085 (p-90) REVERT: D 87 MET cc_start: 0.7041 (mtm) cc_final: 0.6741 (mtm) REVERT: D 134 TYR cc_start: 0.7976 (t80) cc_final: 0.7747 (t80) REVERT: D 180 TRP cc_start: 0.7148 (m100) cc_final: 0.6652 (m100) REVERT: P 120 SER cc_start: 0.8561 (m) cc_final: 0.8358 (p) REVERT: P 187 ASP cc_start: 0.8449 (t0) cc_final: 0.7932 (m-30) REVERT: P 252 ASP cc_start: 0.7250 (p0) cc_final: 0.6910 (p0) REVERT: P 260 LEU cc_start: 0.9450 (mp) cc_final: 0.9198 (mm) REVERT: P 374 PHE cc_start: 0.9006 (t80) cc_final: 0.8730 (t80) REVERT: Q 28 GLN cc_start: 0.6986 (tp-100) cc_final: 0.6674 (tp40) REVERT: Q 47 THR cc_start: 0.7897 (p) cc_final: 0.7585 (p) REVERT: Q 134 TYR cc_start: 0.8684 (t80) cc_final: 0.8434 (t80) REVERT: Q 155 ASN cc_start: 0.6186 (t0) cc_final: 0.5071 (t0) REVERT: Q 214 MET cc_start: 0.8020 (tpp) cc_final: 0.7595 (tpt) outliers start: 2 outliers final: 2 residues processed: 343 average time/residue: 0.2403 time to fit residues: 119.4375 Evaluate side-chains 243 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 241 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 136 optimal weight: 0.0870 chunk 110 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 36 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 284 ASN ** Q 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13509 Z= 0.197 Angle : 0.658 11.088 18520 Z= 0.315 Chirality : 0.043 0.162 1970 Planarity : 0.005 0.055 2327 Dihedral : 8.184 84.318 1858 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.34 % Favored : 88.54 % Rotamer: Outliers : 0.08 % Allowed : 2.96 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.83 (0.21), residues: 1658 helix: 1.20 (0.19), residues: 783 sheet: -0.63 (0.69), residues: 58 loop : -2.44 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 151 HIS 0.005 0.001 HIS C 291 PHE 0.010 0.001 PHE P 105 TYR 0.014 0.001 TYR C 109 ARG 0.006 0.001 ARG Q 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 ASN cc_start: 0.6698 (p0) cc_final: 0.5321 (t0) REVERT: C 39 LYS cc_start: 0.6719 (mttt) cc_final: 0.5622 (tttm) REVERT: C 46 ILE cc_start: 0.7932 (pt) cc_final: 0.7591 (mm) REVERT: C 70 THR cc_start: 0.8781 (m) cc_final: 0.8444 (p) REVERT: C 93 MET cc_start: 0.8542 (mmm) cc_final: 0.8311 (mmm) REVERT: C 175 SER cc_start: 0.8581 (m) cc_final: 0.8314 (t) REVERT: C 199 TYR cc_start: 0.8980 (t80) cc_final: 0.8393 (t80) REVERT: C 296 TRP cc_start: 0.8401 (p-90) cc_final: 0.8090 (p-90) REVERT: D 27 PHE cc_start: 0.7793 (t80) cc_final: 0.7484 (t80) REVERT: D 87 MET cc_start: 0.7127 (mtm) cc_final: 0.6816 (mtm) REVERT: P 260 LEU cc_start: 0.9383 (mp) cc_final: 0.9168 (mt) REVERT: P 305 LEU cc_start: 0.8402 (mt) cc_final: 0.8017 (mt) REVERT: Q 28 GLN cc_start: 0.7014 (tp-100) cc_final: 0.6740 (tp-100) REVERT: Q 47 THR cc_start: 0.7743 (p) cc_final: 0.7504 (p) REVERT: Q 155 ASN cc_start: 0.6597 (t0) cc_final: 0.5443 (t0) outliers start: 1 outliers final: 1 residues processed: 339 average time/residue: 0.2323 time to fit residues: 115.1558 Evaluate side-chains 240 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 59.0825 > 50: distance: 61 - 63: 14.981 distance: 63 - 64: 4.421 distance: 64 - 65: 5.024 distance: 64 - 67: 9.974 distance: 65 - 66: 17.193 distance: 65 - 68: 8.851 distance: 68 - 69: 12.195 distance: 69 - 70: 7.953 distance: 69 - 72: 8.972 distance: 70 - 71: 21.490 distance: 70 - 73: 21.011 distance: 73 - 74: 27.147 distance: 74 - 75: 24.050 distance: 74 - 77: 24.165 distance: 75 - 76: 21.199 distance: 75 - 78: 12.606 distance: 78 - 79: 20.299 distance: 79 - 80: 17.902 distance: 79 - 82: 24.968 distance: 80 - 83: 11.108 distance: 81 - 114: 17.274 distance: 83 - 84: 5.941 distance: 84 - 85: 7.161 distance: 84 - 87: 20.730 distance: 85 - 86: 11.937 distance: 85 - 92: 7.407 distance: 86 - 118: 13.419 distance: 87 - 88: 9.062 distance: 88 - 89: 12.916 distance: 89 - 90: 19.626 distance: 90 - 91: 15.195 distance: 92 - 93: 9.289 distance: 93 - 94: 8.360 distance: 93 - 96: 13.739 distance: 94 - 95: 3.361 distance: 94 - 103: 7.724 distance: 95 - 125: 9.043 distance: 96 - 97: 14.273 distance: 97 - 98: 10.575 distance: 97 - 99: 21.662 distance: 98 - 100: 23.110 distance: 99 - 101: 8.756 distance: 100 - 102: 13.859 distance: 101 - 102: 4.515 distance: 103 - 104: 10.602 distance: 104 - 105: 9.964 distance: 104 - 107: 5.497 distance: 105 - 106: 3.262 distance: 105 - 114: 8.738 distance: 106 - 133: 6.530 distance: 107 - 108: 8.636 distance: 108 - 110: 20.709 distance: 109 - 111: 10.154 distance: 110 - 112: 17.366 distance: 111 - 113: 7.729 distance: 112 - 113: 5.165 distance: 114 - 115: 12.738 distance: 115 - 116: 12.839 distance: 116 - 118: 8.964 distance: 117 - 138: 4.768 distance: 118 - 119: 4.170 distance: 119 - 120: 16.444 distance: 119 - 122: 5.444 distance: 120 - 121: 11.404 distance: 120 - 125: 14.540 distance: 121 - 145: 9.864 distance: 122 - 123: 13.627 distance: 122 - 124: 9.078 distance: 125 - 126: 10.407 distance: 126 - 127: 4.219 distance: 126 - 129: 8.603 distance: 127 - 128: 4.660 distance: 127 - 133: 3.796 distance: 128 - 156: 8.118 distance: 129 - 130: 11.016 distance: 129 - 131: 19.651 distance: 130 - 132: 15.829