Starting phenix.real_space_refine on Sun Aug 4 12:50:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/08_2024/7kr5_23002.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/08_2024/7kr5_23002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/08_2024/7kr5_23002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/08_2024/7kr5_23002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/08_2024/7kr5_23002.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/08_2024/7kr5_23002.cif" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.138 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 Ca 1 9.91 5 S 90 5.16 5 C 6871 2.51 5 N 1660 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 178": "OE1" <-> "OE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 75": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "M ARG 75": "NH1" <-> "NH2" Residue "M ARG 92": "NH1" <-> "NH2" Residue "M PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 75": "NH1" <-> "NH2" Residue "O ARG 92": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10534 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 947 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 944 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 947 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 944 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 947 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 944 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 841 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 777 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 840 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "N" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 777 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "O" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 848 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain breaks: 2 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "P" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 777 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.28, per 1000 atoms: 0.60 Number of scatterers: 10534 At special positions: 0 Unit cell: (116.684, 114.942, 107.105, 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) Ca 1 19.99 S 90 16.00 O 1912 8.00 N 1660 7.00 C 6871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS H 121 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.03 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 108 " distance=2.03 Simple disulfide: pdb=" SG CYS O 45 " - pdb=" SG CYS O 121 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 108 " 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=0, symmetry=0 Time building additional restraints: 4.56 Conformation dependent library (CDL) restraints added in 2.5 seconds 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 47.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 157 through 178 Processing helix chain 'A' and resid 188 through 216 removed outlier: 3.621A pdb=" N ILE A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 272 Processing helix chain 'A' and resid 275 through 304 Proline residue: A 288 - end of helix Processing helix chain 'B' and resid 157 through 178 removed outlier: 3.642A pdb=" N GLU B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 215 removed outlier: 3.668A pdb=" N LEU B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 272 Processing helix chain 'B' and resid 275 through 303 removed outlier: 3.601A pdb=" N ALA B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) Proline residue: B 288 - end of helix Processing helix chain 'C' and resid 157 through 178 Processing helix chain 'C' and resid 188 through 216 removed outlier: 3.621A pdb=" N ILE C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 272 Processing helix chain 'C' and resid 275 through 304 Proline residue: C 288 - end of helix Processing helix chain 'D' and resid 157 through 178 removed outlier: 3.642A pdb=" N GLU D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 215 removed outlier: 3.667A pdb=" N LEU D 192 " --> pdb=" O PRO D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 272 Processing helix chain 'D' and resid 275 through 303 removed outlier: 3.599A pdb=" N ALA D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Proline residue: D 288 - end of helix Processing helix chain 'E' and resid 157 through 178 Processing helix chain 'E' and resid 188 through 216 removed outlier: 3.621A pdb=" N ILE E 216 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 272 Processing helix chain 'E' and resid 275 through 304 Proline residue: E 288 - end of helix Processing helix chain 'F' and resid 157 through 178 removed outlier: 3.643A pdb=" N GLU F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 215 removed outlier: 3.667A pdb=" N LEU F 192 " --> pdb=" O PRO F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 272 Processing helix chain 'F' and resid 275 through 303 removed outlier: 3.600A pdb=" N ALA F 279 " --> pdb=" O SER F 275 " (cutoff:3.500A) Proline residue: F 288 - end of helix Processing helix chain 'H' and resid 51 through 55 Processing helix chain 'M' and resid 51 through 55 Processing helix chain 'O' and resid 51 through 55 removed outlier: 3.634A pdb=" N TYR O 55 " --> pdb=" O PHE O 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 26 through 29 Processing sheet with id=AA2, first strand: chain 'H' and resid 82 through 85 removed outlier: 4.034A pdb=" N ALA H 82 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP H 59 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG H 73 " --> pdb=" O MET H 57 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET H 57 " --> pdb=" O ARG H 73 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA H 56 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 39 through 44 removed outlier: 3.641A pdb=" N ASP L 90 " --> pdb=" O SER L 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 73 through 74 removed outlier: 6.452A pdb=" N TRP L 55 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN L 69 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL L 53 " --> pdb=" O ASN L 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 26 through 29 Processing sheet with id=AA6, first strand: chain 'M' and resid 82 through 85 removed outlier: 3.999A pdb=" N ALA M 82 " --> pdb=" O ARG M 75 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP M 59 " --> pdb=" O VAL M 71 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG M 73 " --> pdb=" O MET M 57 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET M 57 " --> pdb=" O ARG M 73 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA M 56 " --> pdb=" O GLN M 124 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR M 132 " --> pdb=" O ARG M 123 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 82 through 85 removed outlier: 3.999A pdb=" N ALA M 82 " --> pdb=" O ARG M 75 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP M 59 " --> pdb=" O VAL M 71 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG M 73 " --> pdb=" O MET M 57 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET M 57 " --> pdb=" O ARG M 73 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA M 56 " --> pdb=" O GLN M 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 39 through 44 removed outlier: 3.641A pdb=" N ASP N 90 " --> pdb=" O SER N 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 73 through 74 removed outlier: 6.451A pdb=" N TRP N 55 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN N 69 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL N 53 " --> pdb=" O ASN N 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 26 through 30 removed outlier: 3.913A pdb=" N SER O 44 " --> pdb=" O SER O 30 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 83 through 85 removed outlier: 6.518A pdb=" N TRP O 59 " --> pdb=" O VAL O 71 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG O 73 " --> pdb=" O MET O 57 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET O 57 " --> pdb=" O ARG O 73 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA O 56 " --> pdb=" O GLN O 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 39 through 44 removed outlier: 3.641A pdb=" N ASP P 90 " --> pdb=" O SER P 87 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 73 through 74 removed outlier: 6.452A pdb=" N TRP P 55 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN P 69 " --> pdb=" O VAL P 53 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL P 53 " --> pdb=" O ASN P 69 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2097 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: 3.31 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2328 1.33 - 1.45: 2435 1.45 - 1.57: 5867 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 10777 Sorted by residual: bond pdb=" N PRO C 288 " pdb=" CD PRO C 288 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.15e+01 bond pdb=" N PRO A 288 " pdb=" CD PRO A 288 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.11e+01 bond pdb=" N PRO E 288 " pdb=" CD PRO E 288 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.11e+01 bond pdb=" C GLU A 262 " pdb=" N ILE A 263 " ideal model delta sigma weight residual 1.335 1.296 0.039 1.26e-02 6.30e+03 9.35e+00 bond pdb=" N LYS M 90 " pdb=" CA LYS M 90 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.42e-02 4.96e+03 5.07e+00 ... (remaining 10772 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.26: 269 106.26 - 113.20: 6060 113.20 - 120.14: 3495 120.14 - 127.08: 4786 127.08 - 134.02: 136 Bond angle restraints: 14746 Sorted by residual: angle pdb=" N VAL E 285 " pdb=" CA VAL E 285 " pdb=" C VAL E 285 " ideal model delta sigma weight residual 113.39 109.19 4.20 1.47e+00 4.63e-01 8.18e+00 angle pdb=" C VAL H 71 " pdb=" N ALA H 72 " pdb=" CA ALA H 72 " ideal model delta sigma weight residual 121.62 117.29 4.33 1.83e+00 2.99e-01 5.60e+00 angle pdb=" C VAL M 71 " pdb=" N ALA M 72 " pdb=" CA ALA M 72 " ideal model delta sigma weight residual 121.62 117.45 4.17 1.83e+00 2.99e-01 5.18e+00 angle pdb=" N LYS M 90 " pdb=" CA LYS M 90 " pdb=" C LYS M 90 " ideal model delta sigma weight residual 113.19 110.64 2.55 1.19e+00 7.06e-01 4.60e+00 angle pdb=" C VAL O 71 " pdb=" N ALA O 72 " pdb=" CA ALA O 72 " ideal model delta sigma weight residual 121.62 117.72 3.90 1.83e+00 2.99e-01 4.55e+00 ... (remaining 14741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 5719 16.65 - 33.29: 365 33.29 - 49.94: 97 49.94 - 66.59: 7 66.59 - 83.23: 8 Dihedral angle restraints: 6196 sinusoidal: 2004 harmonic: 4192 Sorted by residual: dihedral pdb=" CA LYS M 125 " pdb=" C LYS M 125 " pdb=" N TYR M 126 " pdb=" CA TYR M 126 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA SER H 88 " pdb=" C SER H 88 " pdb=" N VAL H 89 " pdb=" CA VAL H 89 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA SER O 88 " pdb=" C SER O 88 " pdb=" N VAL O 89 " pdb=" CA VAL O 89 " ideal model delta harmonic sigma weight residual 180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 6193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1133 0.029 - 0.057: 438 0.057 - 0.086: 156 0.086 - 0.115: 63 0.115 - 0.144: 7 Chirality restraints: 1797 Sorted by residual: chirality pdb=" CA VAL M 122 " pdb=" N VAL M 122 " pdb=" C VAL M 122 " pdb=" CB VAL M 122 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE P 95 " pdb=" N ILE P 95 " pdb=" C ILE P 95 " pdb=" CB ILE P 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE N 95 " pdb=" N ILE N 95 " pdb=" C ILE N 95 " pdb=" CB ILE N 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1794 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 287 " -0.025 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO D 288 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 287 " -0.025 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 288 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 287 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO F 288 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 288 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 288 " 0.020 5.00e-02 4.00e+02 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 923 2.74 - 3.28: 11145 3.28 - 3.82: 17711 3.82 - 4.36: 19696 4.36 - 4.90: 34607 Nonbonded interactions: 84082 Sorted by model distance: nonbonded pdb=" OG SER F 161 " pdb=" OG1 THR F 252 " model vdw 2.197 3.040 nonbonded pdb=" OG SER D 161 " pdb=" OG1 THR D 252 " model vdw 2.197 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OG1 THR B 252 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR H 51 " pdb=" OG1 THR H 54 " model vdw 2.257 3.040 nonbonded pdb=" O ASP E 182 " pdb=" OG1 THR E 185 " model vdw 2.260 3.040 ... (remaining 84077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 297 or (resid 298 and (name N or name CA or na \ me C or name O or name CB )) or resid 299 through 305)) selection = chain 'B' selection = (chain 'C' and (resid 156 through 297 or (resid 298 and (name N or name CA or na \ me C or name O or name CB )) or resid 299 through 305)) selection = chain 'D' selection = (chain 'E' and (resid 156 through 297 or (resid 298 and (name N or name CA or na \ me C or name O or name CB )) or resid 299 through 305)) selection = chain 'F' } ncs_group { reference = (chain 'H' and (resid 25 through 62 or resid 66 through 145)) selection = (chain 'M' and (resid 25 through 62 or resid 66 through 145)) selection = (chain 'O' and (resid 25 through 62 or resid 66 through 145)) } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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=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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.140 Find NCS groups from input model: 0.500 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.004 0.048 10777 Z= 0.252 Angle : 0.566 6.218 14746 Z= 0.309 Chirality : 0.037 0.144 1797 Planarity : 0.004 0.037 1802 Dihedral : 12.417 83.234 3457 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.77 % Allowed : 6.33 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: -0.04 (0.23), residues: 1390 helix: 1.73 (0.19), residues: 660 sheet: -1.49 (0.28), residues: 307 loop : -1.66 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 70 HIS 0.004 0.001 HIS D 299 PHE 0.007 0.001 PHE L 82 TYR 0.008 0.002 TYR N 73 ARG 0.002 0.001 ARG M 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 304 time to evaluate : 1.113 Fit side-chains REVERT: B 193 ILE cc_start: 0.8038 (mt) cc_final: 0.7736 (mt) REVERT: C 250 PHE cc_start: 0.8203 (t80) cc_final: 0.7779 (t80) REVERT: E 268 TRP cc_start: 0.8216 (t-100) cc_final: 0.7981 (t-100) REVERT: E 296 PHE cc_start: 0.6908 (t80) cc_final: 0.6696 (t80) REVERT: H 28 VAL cc_start: 0.8429 (t) cc_final: 0.8176 (m) REVERT: H 118 MET cc_start: 0.7558 (mtp) cc_final: 0.7168 (mtt) REVERT: H 125 LYS cc_start: 0.8691 (ptmt) cc_final: 0.8338 (ptmm) REVERT: M 103 MET cc_start: 0.8160 (mmt) cc_final: 0.7846 (mmm) REVERT: M 126 TYR cc_start: 0.8501 (t80) cc_final: 0.8288 (t80) REVERT: N 99 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7367 (mm-40) REVERT: O 40 SER cc_start: 0.8195 (m) cc_final: 0.7896 (m) REVERT: O 118 MET cc_start: 0.7548 (mtp) cc_final: 0.7218 (mtt) outliers start: 8 outliers final: 1 residues processed: 305 average time/residue: 0.1594 time to fit residues: 74.9814 Evaluate side-chains 237 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 124 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN E 180 GLN H 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10777 Z= 0.350 Angle : 0.647 7.078 14746 Z= 0.342 Chirality : 0.043 0.145 1797 Planarity : 0.004 0.042 1802 Dihedral : 4.587 27.610 1492 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.74 % Allowed : 15.26 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.11 (0.23), residues: 1390 helix: 1.99 (0.18), residues: 666 sheet: -1.44 (0.27), residues: 306 loop : -1.89 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 70 HIS 0.008 0.001 HIS H 58 PHE 0.019 0.002 PHE M 52 TYR 0.021 0.002 TYR H 126 ARG 0.003 0.001 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 233 time to evaluate : 1.063 Fit side-chains REVERT: A 283 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7774 (t) REVERT: C 168 LEU cc_start: 0.8018 (mt) cc_final: 0.7607 (pp) REVERT: C 250 PHE cc_start: 0.8239 (t80) cc_final: 0.7893 (t80) REVERT: E 168 LEU cc_start: 0.7692 (mt) cc_final: 0.7462 (pp) REVERT: E 262 GLU cc_start: 0.8780 (tp30) cc_final: 0.8517 (tm-30) REVERT: H 28 VAL cc_start: 0.8435 (t) cc_final: 0.8193 (m) REVERT: H 118 MET cc_start: 0.7655 (mtp) cc_final: 0.7255 (mtt) REVERT: H 125 LYS cc_start: 0.8878 (ptmt) cc_final: 0.8556 (ptmm) REVERT: N 99 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7418 (mm-40) REVERT: O 118 MET cc_start: 0.7592 (mtp) cc_final: 0.7209 (mtt) REVERT: O 125 LYS cc_start: 0.8742 (ptmm) cc_final: 0.8459 (ptmm) outliers start: 39 outliers final: 25 residues processed: 249 average time/residue: 0.1630 time to fit residues: 62.4457 Evaluate side-chains 241 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 ASN P 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10777 Z= 0.284 Angle : 0.590 6.675 14746 Z= 0.311 Chirality : 0.041 0.138 1797 Planarity : 0.004 0.044 1802 Dihedral : 4.235 18.343 1489 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.80 % Allowed : 17.47 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.53 (0.23), residues: 1390 helix: 2.36 (0.18), residues: 666 sheet: -1.25 (0.28), residues: 316 loop : -1.71 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 70 HIS 0.008 0.001 HIS H 58 PHE 0.011 0.002 PHE P 107 TYR 0.017 0.002 TYR H 126 ARG 0.002 0.001 ARG P 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 1.109 Fit side-chains REVERT: A 268 TRP cc_start: 0.8315 (t-100) cc_final: 0.7987 (t-100) REVERT: C 176 MET cc_start: 0.8568 (tmm) cc_final: 0.8209 (ttt) REVERT: C 250 PHE cc_start: 0.8282 (t80) cc_final: 0.7961 (t80) REVERT: C 254 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6380 (tt) REVERT: D 176 MET cc_start: 0.9018 (tmm) cc_final: 0.8779 (tmm) REVERT: E 163 LYS cc_start: 0.8576 (tptm) cc_final: 0.8163 (tptp) REVERT: E 168 LEU cc_start: 0.7892 (mt) cc_final: 0.7332 (pp) REVERT: H 28 VAL cc_start: 0.8458 (t) cc_final: 0.8197 (m) REVERT: H 118 MET cc_start: 0.7636 (mtp) cc_final: 0.7240 (mtt) REVERT: H 125 LYS cc_start: 0.8829 (ptmt) cc_final: 0.8545 (ptmm) REVERT: N 99 GLN cc_start: 0.7755 (mm-40) cc_final: 0.6588 (mm-40) REVERT: O 118 MET cc_start: 0.7626 (mtp) cc_final: 0.7140 (mtt) REVERT: O 125 LYS cc_start: 0.8749 (ptmm) cc_final: 0.8437 (ptmm) outliers start: 50 outliers final: 27 residues processed: 257 average time/residue: 0.1689 time to fit residues: 66.2136 Evaluate side-chains 244 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 267 CYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.1980 chunk 92 optimal weight: 0.0170 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 130 optimal weight: 0.0010 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 62 GLN P 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10777 Z= 0.147 Angle : 0.537 6.634 14746 Z= 0.278 Chirality : 0.039 0.133 1797 Planarity : 0.004 0.043 1802 Dihedral : 3.885 17.134 1489 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.07 % Allowed : 19.10 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 1.13 (0.23), residues: 1390 helix: 2.83 (0.18), residues: 666 sheet: -0.71 (0.29), residues: 301 loop : -1.63 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 280 HIS 0.006 0.001 HIS O 58 PHE 0.009 0.001 PHE A 259 TYR 0.011 0.001 TYR H 126 ARG 0.002 0.000 ARG O 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 244 time to evaluate : 1.175 Fit side-chains REVERT: B 258 LEU cc_start: 0.7431 (mt) cc_final: 0.7149 (mt) REVERT: C 176 MET cc_start: 0.8566 (tmm) cc_final: 0.8247 (ttt) REVERT: C 250 PHE cc_start: 0.8257 (t80) cc_final: 0.7911 (t80) REVERT: E 163 LYS cc_start: 0.8589 (tptm) cc_final: 0.8182 (tptp) REVERT: E 168 LEU cc_start: 0.7882 (mt) cc_final: 0.7347 (pp) REVERT: H 28 VAL cc_start: 0.8520 (t) cc_final: 0.8283 (m) REVERT: H 57 MET cc_start: 0.7828 (mmm) cc_final: 0.7566 (mmm) REVERT: H 118 MET cc_start: 0.7547 (mtp) cc_final: 0.7154 (mtt) REVERT: H 125 LYS cc_start: 0.8714 (ptmt) cc_final: 0.8299 (ptmm) REVERT: N 99 GLN cc_start: 0.7704 (mm-40) cc_final: 0.6741 (mm-40) REVERT: O 118 MET cc_start: 0.7603 (mtp) cc_final: 0.7168 (mtt) REVERT: O 125 LYS cc_start: 0.8597 (ptmm) cc_final: 0.8318 (ptmm) outliers start: 32 outliers final: 21 residues processed: 258 average time/residue: 0.1650 time to fit residues: 65.1410 Evaluate side-chains 241 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 267 CYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.0670 chunk 117 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN M 62 GLN P 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10777 Z= 0.256 Angle : 0.588 6.826 14746 Z= 0.301 Chirality : 0.040 0.158 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.905 17.612 1489 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.03 % Allowed : 21.02 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 1.04 (0.23), residues: 1390 helix: 2.76 (0.18), residues: 666 sheet: -0.81 (0.29), residues: 310 loop : -1.61 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 70 HIS 0.006 0.001 HIS M 58 PHE 0.014 0.001 PHE D 171 TYR 0.014 0.002 TYR H 126 ARG 0.002 0.001 ARG H 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 1.709 Fit side-chains REVERT: A 176 MET cc_start: 0.8597 (tmm) cc_final: 0.8263 (ttt) REVERT: C 176 MET cc_start: 0.8559 (tmm) cc_final: 0.8342 (ttt) REVERT: C 250 PHE cc_start: 0.8282 (t80) cc_final: 0.7955 (t80) REVERT: D 176 MET cc_start: 0.9019 (tmm) cc_final: 0.8727 (tmm) REVERT: E 163 LYS cc_start: 0.8618 (tptm) cc_final: 0.8227 (tptp) REVERT: H 28 VAL cc_start: 0.8572 (t) cc_final: 0.8320 (m) REVERT: H 57 MET cc_start: 0.7965 (mmm) cc_final: 0.7686 (mmm) REVERT: H 118 MET cc_start: 0.7608 (mtp) cc_final: 0.7197 (mtt) REVERT: H 125 LYS cc_start: 0.8842 (ptmt) cc_final: 0.8431 (ptmm) REVERT: M 54 THR cc_start: 0.8327 (p) cc_final: 0.8023 (t) REVERT: N 99 GLN cc_start: 0.7716 (mm-40) cc_final: 0.6804 (mm-40) REVERT: O 118 MET cc_start: 0.7610 (mtp) cc_final: 0.7134 (mtt) REVERT: O 125 LYS cc_start: 0.8725 (ptmm) cc_final: 0.8415 (ptmm) outliers start: 42 outliers final: 33 residues processed: 251 average time/residue: 0.1746 time to fit residues: 68.2098 Evaluate side-chains 250 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 217 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 267 CYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 52.7695 > 50: distance: 49 - 77: 4.196 distance: 52 - 74: 5.727 distance: 59 - 63: 11.986 distance: 63 - 64: 21.183 distance: 64 - 65: 15.587 distance: 64 - 67: 18.552 distance: 65 - 66: 4.196 distance: 65 - 68: 20.104 distance: 68 - 69: 16.101 distance: 69 - 70: 12.758 distance: 69 - 72: 9.581 distance: 70 - 71: 12.099 distance: 70 - 74: 14.195 distance: 72 - 73: 9.731 distance: 74 - 75: 10.217 distance: 75 - 76: 16.038 distance: 75 - 78: 7.085 distance: 76 - 77: 7.028 distance: 76 - 86: 8.297 distance: 78 - 79: 6.804 distance: 79 - 80: 14.542 distance: 79 - 81: 27.016 distance: 80 - 82: 4.845 distance: 81 - 83: 6.710 distance: 82 - 84: 20.832 distance: 83 - 84: 21.180 distance: 84 - 85: 8.304 distance: 86 - 87: 11.925 distance: 87 - 88: 12.022 distance: 87 - 90: 14.735 distance: 88 - 89: 18.313 distance: 88 - 97: 6.306 distance: 90 - 91: 10.046 distance: 91 - 92: 7.807 distance: 93 - 94: 5.358 distance: 94 - 95: 9.100 distance: 94 - 96: 4.485 distance: 97 - 98: 3.780 distance: 98 - 99: 26.666 distance: 98 - 101: 6.799 distance: 99 - 100: 21.254 distance: 99 - 105: 11.996 distance: 101 - 102: 13.229 distance: 102 - 103: 3.403 distance: 102 - 104: 8.567 distance: 105 - 106: 20.659 distance: 106 - 107: 12.997 distance: 106 - 109: 13.911 distance: 107 - 108: 3.597 distance: 107 - 111: 9.435 distance: 109 - 110: 23.172 distance: 111 - 112: 21.935 distance: 112 - 113: 17.190 distance: 113 - 114: 3.687 distance: 113 - 115: 11.520 distance: 115 - 116: 7.911 distance: 116 - 117: 20.544 distance: 116 - 119: 16.888 distance: 117 - 118: 17.813 distance: 117 - 122: 4.348 distance: 119 - 120: 9.373 distance: 119 - 121: 22.781 distance: 122 - 123: 6.439 distance: 122 - 128: 8.760 distance: 123 - 124: 15.342 distance: 123 - 126: 14.498 distance: 124 - 125: 7.917 distance: 124 - 129: 5.299 distance: 126 - 127: 9.769 distance: 127 - 128: 15.239 distance: 129 - 130: 3.073 distance: 130 - 131: 7.988 distance: 130 - 133: 7.657 distance: 131 - 137: 6.105 distance: 133 - 134: 5.637 distance: 134 - 135: 3.354 distance: 134 - 136: 3.060