Starting phenix.real_space_refine on Wed Feb 14 23:29:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/02_2024/7kr5_23002.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/02_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_23002/02_2024/7kr5_23002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/02_2024/7kr5_23002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/02_2024/7kr5_23002.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kr5_23002/02_2024/7kr5_23002.pdb" } 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-5238/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: 5.82, per 1000 atoms: 0.55 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: 4.87 Conformation dependent library (CDL) restraints added in 2.2 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: 5.21 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 2.440 nonbonded pdb=" OG SER D 161 " pdb=" OG1 THR D 252 " model vdw 2.197 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OG1 THR B 252 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR H 51 " pdb=" OG1 THR H 54 " model vdw 2.257 2.440 nonbonded pdb=" O ASP E 182 " pdb=" OG1 THR E 185 " model vdw 2.260 2.440 ... (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 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: 0.860 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: 4.700 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.680 Find NCS groups from input model: 0.840 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.270 ------------------------------------------------------------------------------- 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 : 1.153 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: 0.1653 time to fit residues: 77.5614 Evaluate side-chains 237 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10777 Z= 0.328 Angle : 0.621 6.581 14746 Z= 0.327 Chirality : 0.041 0.139 1797 Planarity : 0.004 0.041 1802 Dihedral : 4.494 32.831 1492 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.41 % Allowed : 14.97 % Favored : 80.61 % 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: 0.22 (0.23), residues: 1390 helix: 2.16 (0.19), residues: 666 sheet: -1.56 (0.27), residues: 314 loop : -1.82 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 70 HIS 0.007 0.001 HIS H 58 PHE 0.018 0.002 PHE E 259 TYR 0.019 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 280 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 234 time to evaluate : 1.262 Fit side-chains REVERT: A 283 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7778 (t) REVERT: C 168 LEU cc_start: 0.8017 (mt) cc_final: 0.7642 (pp) REVERT: C 250 PHE cc_start: 0.8218 (t80) cc_final: 0.7866 (t80) REVERT: E 168 LEU cc_start: 0.7713 (mt) cc_final: 0.7509 (pp) REVERT: E 262 GLU cc_start: 0.8783 (tp30) cc_final: 0.8512 (tm-30) REVERT: H 28 VAL cc_start: 0.8511 (t) cc_final: 0.8246 (m) REVERT: H 118 MET cc_start: 0.7661 (mtp) cc_final: 0.7265 (mtt) REVERT: H 125 LYS cc_start: 0.8802 (ptmt) cc_final: 0.8450 (ptmm) REVERT: L 99 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7397 (mm-40) REVERT: M 103 MET cc_start: 0.8226 (mmt) cc_final: 0.8004 (mmm) REVERT: N 99 GLN cc_start: 0.7775 (mm-40) cc_final: 0.6526 (mm-40) REVERT: O 118 MET cc_start: 0.7593 (mtp) cc_final: 0.7215 (mtt) REVERT: O 125 LYS cc_start: 0.8661 (ptmm) cc_final: 0.8449 (ptmm) REVERT: P 125 GLU cc_start: 0.6748 (tp30) cc_final: 0.6068 (tm-30) outliers start: 46 outliers final: 25 residues processed: 255 average time/residue: 0.1755 time to fit residues: 67.8575 Evaluate side-chains 245 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 219 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 C residue 273 ASP Chi-restraints excluded: chain D residue 257 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 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 44 SER Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 112 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 102 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.9084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10777 Z= 0.174 Angle : 0.536 6.665 14746 Z= 0.279 Chirality : 0.038 0.133 1797 Planarity : 0.004 0.042 1802 Dihedral : 4.052 18.802 1489 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.74 % Allowed : 17.37 % Favored : 78.89 % 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: 0.78 (0.23), residues: 1390 helix: 2.65 (0.19), residues: 666 sheet: -1.29 (0.28), residues: 301 loop : -1.63 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 70 HIS 0.007 0.001 HIS M 58 PHE 0.008 0.001 PHE P 107 TYR 0.015 0.001 TYR H 126 ARG 0.002 0.000 ARG O 73 *********************** 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 282 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 243 time to evaluate : 1.046 Fit side-chains REVERT: B 193 ILE cc_start: 0.8134 (mt) cc_final: 0.7911 (mt) REVERT: B 258 LEU cc_start: 0.7550 (mt) cc_final: 0.7287 (mt) REVERT: C 168 LEU cc_start: 0.8049 (mt) cc_final: 0.7600 (pp) REVERT: C 250 PHE cc_start: 0.8249 (t80) cc_final: 0.7881 (t80) REVERT: E 168 LEU cc_start: 0.7805 (mt) cc_final: 0.7452 (pp) REVERT: H 28 VAL cc_start: 0.8579 (t) cc_final: 0.8336 (m) REVERT: H 118 MET cc_start: 0.7640 (mtp) cc_final: 0.7248 (mtt) REVERT: H 125 LYS cc_start: 0.8716 (ptmt) cc_final: 0.8294 (ptmm) REVERT: N 99 GLN cc_start: 0.7679 (mm-40) cc_final: 0.6592 (mm-40) REVERT: O 118 MET cc_start: 0.7532 (mtp) cc_final: 0.7180 (mtt) REVERT: O 125 LYS cc_start: 0.8571 (ptmm) cc_final: 0.8317 (ptmm) outliers start: 39 outliers final: 23 residues processed: 258 average time/residue: 0.1704 time to fit residues: 66.4747 Evaluate side-chains 251 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 254 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 256 LEU 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 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: 1.9990 chunk 92 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 82 optimal weight: 0.9980 chunk 123 optimal weight: 0.0870 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10777 Z= 0.145 Angle : 0.521 6.859 14746 Z= 0.267 Chirality : 0.037 0.129 1797 Planarity : 0.004 0.043 1802 Dihedral : 3.761 18.064 1489 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.98 % Allowed : 19.19 % 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: 1.21 (0.24), residues: 1390 helix: 2.94 (0.18), residues: 666 sheet: -1.01 (0.28), residues: 313 loop : -1.37 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 280 HIS 0.005 0.001 HIS O 58 PHE 0.010 0.001 PHE D 171 TYR 0.011 0.001 TYR H 126 ARG 0.003 0.000 ARG M 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 279 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 248 time to evaluate : 1.163 Fit side-chains REVERT: B 193 ILE cc_start: 0.8130 (mt) cc_final: 0.7898 (mt) REVERT: B 258 LEU cc_start: 0.7491 (mt) cc_final: 0.7229 (mt) REVERT: C 168 LEU cc_start: 0.8016 (mt) cc_final: 0.7572 (pp) REVERT: C 176 MET cc_start: 0.8516 (tmm) cc_final: 0.8194 (ttt) REVERT: C 250 PHE cc_start: 0.8247 (t80) cc_final: 0.7897 (t80) REVERT: E 168 LEU cc_start: 0.7857 (mt) cc_final: 0.7470 (pp) REVERT: E 268 TRP cc_start: 0.8317 (t-100) cc_final: 0.7870 (t-100) REVERT: H 28 VAL cc_start: 0.8591 (t) cc_final: 0.8356 (m) REVERT: H 118 MET cc_start: 0.7588 (mtp) cc_final: 0.7228 (mtt) REVERT: H 125 LYS cc_start: 0.8676 (ptmt) cc_final: 0.8281 (ptmm) REVERT: L 80 ASP cc_start: 0.7812 (t0) cc_final: 0.7608 (t0) REVERT: M 103 MET cc_start: 0.7737 (mmm) cc_final: 0.7271 (mmm) REVERT: N 99 GLN cc_start: 0.7680 (mm-40) cc_final: 0.6801 (mm-40) REVERT: O 118 MET cc_start: 0.7526 (mtp) cc_final: 0.7179 (mtt) REVERT: O 125 LYS cc_start: 0.8528 (ptmm) cc_final: 0.8276 (ptmm) REVERT: P 125 GLU cc_start: 0.6344 (tp30) cc_final: 0.5687 (tm-30) outliers start: 31 outliers final: 21 residues processed: 266 average time/residue: 0.1736 time to fit residues: 70.0391 Evaluate side-chains 253 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 263 ILE 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 256 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 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 P residue 25 THR Chi-restraints excluded: chain P residue 46 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 117 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10777 Z= 0.179 Angle : 0.538 6.787 14746 Z= 0.274 Chirality : 0.038 0.129 1797 Planarity : 0.004 0.044 1802 Dihedral : 3.725 18.182 1489 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.88 % Allowed : 20.15 % Favored : 76.97 % 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: 1.36 (0.24), residues: 1390 helix: 3.06 (0.18), residues: 666 sheet: -0.87 (0.29), residues: 313 loop : -1.35 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 70 HIS 0.005 0.001 HIS M 58 PHE 0.012 0.001 PHE D 171 TYR 0.013 0.001 TYR H 126 ARG 0.002 0.000 ARG O 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 264 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 234 time to evaluate : 1.071 Fit side-chains REVERT: B 173 MET cc_start: 0.7658 (mmm) cc_final: 0.7190 (tpt) REVERT: B 176 MET cc_start: 0.8790 (tmm) cc_final: 0.8384 (tmm) REVERT: B 258 LEU cc_start: 0.7454 (mt) cc_final: 0.7129 (mt) REVERT: C 168 LEU cc_start: 0.8058 (mt) cc_final: 0.7513 (pp) REVERT: C 176 MET cc_start: 0.8537 (tmm) cc_final: 0.8244 (ttt) REVERT: C 250 PHE cc_start: 0.8268 (t80) cc_final: 0.7948 (t80) REVERT: C 254 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6442 (tt) REVERT: E 163 LYS cc_start: 0.8615 (tptm) cc_final: 0.8248 (tptp) REVERT: E 168 LEU cc_start: 0.7928 (mt) cc_final: 0.7424 (pp) REVERT: H 28 VAL cc_start: 0.8583 (t) cc_final: 0.8353 (m) REVERT: H 118 MET cc_start: 0.7580 (mtp) cc_final: 0.7186 (mtt) REVERT: H 125 LYS cc_start: 0.8715 (ptmt) cc_final: 0.8320 (ptmm) REVERT: L 62 GLN cc_start: 0.8203 (mp10) cc_final: 0.7963 (mp10) REVERT: L 80 ASP cc_start: 0.7790 (t0) cc_final: 0.7555 (t0) REVERT: M 103 MET cc_start: 0.7757 (mmm) cc_final: 0.7239 (mmm) REVERT: N 99 GLN cc_start: 0.7732 (mm-40) cc_final: 0.6952 (mm-40) REVERT: O 118 MET cc_start: 0.7558 (mtp) cc_final: 0.7178 (mtt) REVERT: O 125 LYS cc_start: 0.8585 (ptmm) cc_final: 0.8314 (ptmm) outliers start: 30 outliers final: 21 residues processed: 249 average time/residue: 0.1755 time to fit residues: 65.7346 Evaluate side-chains 248 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 267 CYS 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 116 THR Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10777 Z= 0.202 Angle : 0.549 7.031 14746 Z= 0.280 Chirality : 0.038 0.156 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.710 17.573 1489 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.65 % Allowed : 20.83 % Favored : 75.53 % 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: 1.45 (0.24), residues: 1390 helix: 3.06 (0.18), residues: 666 sheet: -0.77 (0.29), residues: 310 loop : -1.22 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 280 HIS 0.006 0.001 HIS M 58 PHE 0.013 0.001 PHE D 171 TYR 0.013 0.001 TYR H 126 ARG 0.002 0.000 ARG O 73 *********************** REFINEMENT MACRO_CYCLE 6 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 270 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 1.251 Fit side-chains REVERT: C 176 MET cc_start: 0.8560 (tmm) cc_final: 0.8336 (ttt) REVERT: C 182 ASP cc_start: 0.7929 (t0) cc_final: 0.7600 (t0) REVERT: C 250 PHE cc_start: 0.8254 (t80) cc_final: 0.7962 (t80) REVERT: C 254 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6488 (tt) REVERT: E 163 LYS cc_start: 0.8630 (tptm) cc_final: 0.8274 (tptp) REVERT: E 168 LEU cc_start: 0.7900 (mt) cc_final: 0.7348 (pp) REVERT: H 28 VAL cc_start: 0.8593 (t) cc_final: 0.8350 (m) REVERT: H 118 MET cc_start: 0.7573 (mtp) cc_final: 0.7186 (mtt) REVERT: H 125 LYS cc_start: 0.8729 (ptmt) cc_final: 0.8324 (ptmm) REVERT: L 80 ASP cc_start: 0.7759 (t0) cc_final: 0.7558 (t0) REVERT: M 103 MET cc_start: 0.7768 (mmm) cc_final: 0.7232 (mmm) REVERT: N 99 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7021 (mm-40) REVERT: O 118 MET cc_start: 0.7601 (mtp) cc_final: 0.7163 (mtt) REVERT: O 125 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8347 (ptmm) outliers start: 38 outliers final: 32 residues processed: 253 average time/residue: 0.1700 time to fit residues: 65.3687 Evaluate side-chains 258 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 224 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 254 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 267 CYS 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 C residue 273 ASP Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 257 ILE 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 256 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 267 CYS Chi-restraints excluded: chain F residue 287 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 O residue 44 SER Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.0870 chunk 74 optimal weight: 0.2980 chunk 95 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 40.0000 chunk 80 optimal weight: 4.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10777 Z= 0.254 Angle : 0.578 7.395 14746 Z= 0.294 Chirality : 0.039 0.226 1797 Planarity : 0.004 0.046 1802 Dihedral : 3.786 18.281 1489 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.13 % Allowed : 20.92 % 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: 1.42 (0.24), residues: 1390 helix: 3.04 (0.18), residues: 666 sheet: -0.70 (0.29), residues: 314 loop : -1.32 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 70 HIS 0.006 0.001 HIS M 58 PHE 0.013 0.001 PHE D 171 TYR 0.014 0.002 TYR H 126 ARG 0.003 0.000 ARG O 73 *********************** REFINEMENT MACRO_CYCLE 7 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 271 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 228 time to evaluate : 1.169 Fit side-chains REVERT: A 176 MET cc_start: 0.8608 (tmm) cc_final: 0.8278 (ttt) REVERT: B 173 MET cc_start: 0.7734 (mmm) cc_final: 0.7441 (tpt) REVERT: B 176 MET cc_start: 0.8788 (tmm) cc_final: 0.8383 (tmm) REVERT: C 182 ASP cc_start: 0.7947 (t0) cc_final: 0.7626 (t0) REVERT: C 250 PHE cc_start: 0.8210 (t80) cc_final: 0.7948 (t80) REVERT: C 254 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6334 (tt) REVERT: E 163 LYS cc_start: 0.8669 (tptm) cc_final: 0.8335 (tptp) REVERT: H 28 VAL cc_start: 0.8616 (t) cc_final: 0.8361 (m) REVERT: H 118 MET cc_start: 0.7560 (mtp) cc_final: 0.7164 (mtt) REVERT: H 125 LYS cc_start: 0.8765 (ptmt) cc_final: 0.8362 (ptmm) REVERT: L 80 ASP cc_start: 0.7747 (t0) cc_final: 0.7545 (t0) REVERT: N 99 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7048 (mm-40) REVERT: O 92 ARG cc_start: 0.7536 (mtm110) cc_final: 0.6743 (mtm110) REVERT: O 118 MET cc_start: 0.7621 (mtp) cc_final: 0.7179 (mtt) REVERT: O 125 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8401 (ptmm) REVERT: P 24 MET cc_start: 0.8443 (mmm) cc_final: 0.7785 (mtp) outliers start: 43 outliers final: 35 residues processed: 252 average time/residue: 0.1763 time to fit residues: 67.4335 Evaluate side-chains 261 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 224 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 287 ILE 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 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 C residue 273 ASP Chi-restraints excluded: chain C residue 285 VAL 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 256 LEU Chi-restraints excluded: chain E residue 273 ASP 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 287 ILE Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 124 GLN 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 O residue 44 SER Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.0050 chunk 77 optimal weight: 0.0030 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 10777 Z= 0.148 Angle : 0.540 7.772 14746 Z= 0.272 Chirality : 0.038 0.186 1797 Planarity : 0.004 0.044 1802 Dihedral : 3.591 17.725 1489 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.78 % Allowed : 23.13 % Favored : 74.09 % 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: 1.77 (0.23), residues: 1390 helix: 3.25 (0.18), residues: 666 sheet: -0.23 (0.30), residues: 298 loop : -1.24 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 280 HIS 0.005 0.001 HIS M 58 PHE 0.021 0.001 PHE E 250 TYR 0.010 0.001 TYR H 126 ARG 0.003 0.000 ARG O 123 *********************** REFINEMENT MACRO_CYCLE 8 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 262 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 1.192 Fit side-chains REVERT: A 176 MET cc_start: 0.8571 (tmm) cc_final: 0.8209 (ttt) REVERT: C 182 ASP cc_start: 0.7903 (t0) cc_final: 0.7605 (t0) REVERT: C 250 PHE cc_start: 0.8248 (t80) cc_final: 0.8001 (t80) REVERT: D 294 MET cc_start: 0.5282 (tpt) cc_final: 0.4772 (tpp) REVERT: E 163 LYS cc_start: 0.8634 (tptm) cc_final: 0.8315 (tptp) REVERT: H 28 VAL cc_start: 0.8585 (t) cc_final: 0.8361 (m) REVERT: H 57 MET cc_start: 0.7837 (mmm) cc_final: 0.7601 (mmm) REVERT: H 118 MET cc_start: 0.7564 (mtp) cc_final: 0.7219 (mtt) REVERT: H 125 LYS cc_start: 0.8676 (ptmt) cc_final: 0.8294 (ptmm) REVERT: N 62 GLN cc_start: 0.7929 (mp10) cc_final: 0.7139 (pt0) REVERT: N 99 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7115 (mt0) REVERT: O 118 MET cc_start: 0.7517 (mtp) cc_final: 0.7121 (mtt) REVERT: O 125 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8310 (ptmm) REVERT: P 24 MET cc_start: 0.8400 (mmm) cc_final: 0.7763 (mtp) REVERT: P 62 GLN cc_start: 0.7968 (mp10) cc_final: 0.7067 (pt0) outliers start: 29 outliers final: 21 residues processed: 249 average time/residue: 0.1810 time to fit residues: 67.3450 Evaluate side-chains 248 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 124 GLN 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 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 44 SER Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.4980 chunk 121 optimal weight: 0.1980 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10777 Z= 0.180 Angle : 0.570 9.680 14746 Z= 0.284 Chirality : 0.039 0.289 1797 Planarity : 0.004 0.075 1802 Dihedral : 3.583 17.745 1489 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.59 % Allowed : 23.42 % Favored : 73.99 % 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: 1.74 (0.23), residues: 1390 helix: 3.25 (0.18), residues: 666 sheet: -0.34 (0.30), residues: 309 loop : -1.24 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 70 HIS 0.005 0.001 HIS M 58 PHE 0.021 0.001 PHE O 52 TYR 0.011 0.001 TYR H 126 ARG 0.005 0.000 ARG O 123 *********************** REFINEMENT MACRO_CYCLE 9 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 252 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 225 time to evaluate : 1.168 Fit side-chains REVERT: A 176 MET cc_start: 0.8576 (tmm) cc_final: 0.8176 (ttt) REVERT: B 173 MET cc_start: 0.7656 (mmm) cc_final: 0.7306 (tpt) REVERT: B 294 MET cc_start: 0.5135 (tpt) cc_final: 0.4864 (tpt) REVERT: C 182 ASP cc_start: 0.7906 (t0) cc_final: 0.7616 (t0) REVERT: C 250 PHE cc_start: 0.8204 (t80) cc_final: 0.7949 (t80) REVERT: D 193 ILE cc_start: 0.7893 (mt) cc_final: 0.7691 (mp) REVERT: D 294 MET cc_start: 0.5264 (tpt) cc_final: 0.4740 (tpp) REVERT: E 163 LYS cc_start: 0.8619 (tptm) cc_final: 0.8325 (tptp) REVERT: E 268 TRP cc_start: 0.8370 (t-100) cc_final: 0.8061 (t-100) REVERT: H 28 VAL cc_start: 0.8627 (t) cc_final: 0.8412 (m) REVERT: H 57 MET cc_start: 0.7869 (mmm) cc_final: 0.7638 (mmm) REVERT: H 118 MET cc_start: 0.7552 (mtp) cc_final: 0.7193 (mtt) REVERT: H 125 LYS cc_start: 0.8743 (ptmt) cc_final: 0.8317 (ptmm) REVERT: M 103 MET cc_start: 0.7505 (mmm) cc_final: 0.7228 (mmm) REVERT: N 99 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7221 (mt0) REVERT: O 92 ARG cc_start: 0.7461 (mtm110) cc_final: 0.6679 (mtm110) REVERT: O 118 MET cc_start: 0.7526 (mtp) cc_final: 0.7105 (mtt) REVERT: O 125 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8303 (ptmm) REVERT: P 24 MET cc_start: 0.8398 (mmm) cc_final: 0.7754 (mtp) REVERT: P 62 GLN cc_start: 0.7939 (mp10) cc_final: 0.7074 (pt0) REVERT: P 125 GLU cc_start: 0.6489 (tp30) cc_final: 0.5779 (tm-30) outliers start: 27 outliers final: 26 residues processed: 237 average time/residue: 0.1864 time to fit residues: 65.7115 Evaluate side-chains 247 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 220 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 285 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 124 GLN 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 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 44 SER Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 134 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10777 Z= 0.157 Angle : 0.564 11.104 14746 Z= 0.278 Chirality : 0.039 0.268 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.516 17.571 1489 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.40 % Allowed : 23.70 % Favored : 73.90 % 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: 1.85 (0.23), residues: 1390 helix: 3.34 (0.18), residues: 666 sheet: -0.36 (0.30), residues: 308 loop : -1.14 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 280 HIS 0.005 0.001 HIS M 58 PHE 0.016 0.001 PHE O 52 TYR 0.010 0.001 TYR H 126 ARG 0.003 0.000 ARG L 81 ********************** REFINEMENT MACRO_CYCLE 10 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 253 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 1.178 Fit side-chains REVERT: B 173 MET cc_start: 0.7622 (mmm) cc_final: 0.7267 (tpt) REVERT: C 182 ASP cc_start: 0.7903 (t0) cc_final: 0.7611 (t0) REVERT: C 250 PHE cc_start: 0.8196 (t80) cc_final: 0.7934 (t80) REVERT: D 176 MET cc_start: 0.9026 (tmm) cc_final: 0.8782 (ppp) REVERT: D 193 ILE cc_start: 0.7862 (mt) cc_final: 0.7644 (mp) REVERT: D 294 MET cc_start: 0.5145 (tpt) cc_final: 0.4598 (tpp) REVERT: E 163 LYS cc_start: 0.8656 (tptm) cc_final: 0.8345 (tptp) REVERT: E 268 TRP cc_start: 0.8347 (t-100) cc_final: 0.8086 (t-100) REVERT: F 290 MET cc_start: 0.7798 (tpp) cc_final: 0.7554 (tpp) REVERT: H 28 VAL cc_start: 0.8593 (t) cc_final: 0.8385 (m) REVERT: H 118 MET cc_start: 0.7527 (mtp) cc_final: 0.7157 (mtt) REVERT: H 125 LYS cc_start: 0.8669 (ptmt) cc_final: 0.8292 (ptmm) REVERT: M 103 MET cc_start: 0.7413 (mmm) cc_final: 0.7160 (mmm) REVERT: N 62 GLN cc_start: 0.7945 (mp10) cc_final: 0.7288 (pt0) REVERT: N 99 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7249 (mt0) REVERT: O 92 ARG cc_start: 0.7393 (mtm110) cc_final: 0.6621 (mtm110) REVERT: O 118 MET cc_start: 0.7522 (mtp) cc_final: 0.7127 (mtt) REVERT: O 125 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8300 (ptmm) REVERT: P 24 MET cc_start: 0.8392 (mmm) cc_final: 0.7807 (mtp) REVERT: P 62 GLN cc_start: 0.7933 (mp10) cc_final: 0.7142 (pt0) outliers start: 25 outliers final: 22 residues processed: 242 average time/residue: 0.1890 time to fit residues: 68.1570 Evaluate side-chains 245 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 124 GLN 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 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 44 SER Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.181373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145926 restraints weight = 13965.134| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.19 r_work: 0.3757 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3524 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= 0.158 Angle : 0.562 11.343 14746 Z= 0.278 Chirality : 0.038 0.245 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.472 17.486 1489 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.69 % Allowed : 23.51 % Favored : 73.80 % 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: 1.94 (0.23), residues: 1390 helix: 3.40 (0.18), residues: 666 sheet: -0.25 (0.31), residues: 308 loop : -1.14 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 70 HIS 0.004 0.001 HIS H 58 PHE 0.016 0.001 PHE O 52 TYR 0.010 0.001 TYR H 126 ARG 0.007 0.000 ARG O 123 =============================================================================== Job complete usr+sys time: 2516.15 seconds wall clock time: 46 minutes 17.78 seconds (2777.78 seconds total)