Starting phenix.real_space_refine on Fri Feb 14 18:41:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kr5_23002/02_2025/7kr5_23002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kr5_23002/02_2025/7kr5_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/cci-nas-00/data/ceres_data/7kr5_23002/02_2025/7kr5_23002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kr5_23002/02_2025/7kr5_23002.map" model { file = "/net/cci-nas-00/data/ceres_data/7kr5_23002/02_2025/7kr5_23002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kr5_23002/02_2025/7kr5_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. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.48, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 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: 2.92 Conformation dependent library (CDL) restraints added in 1.3 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: 1.08 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: 3.29 Time building geometry restraints manager: 3.35 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: 0.00 - 1.24: 14157 1.24 - 2.49: 481 2.49 - 3.73: 80 3.73 - 4.97: 13 4.97 - 6.22: 15 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: 1.400 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.770 Find NCS groups from input model: 0.700 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 8 poor density : 304 time to evaluate : 1.342 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: 0.1650 time to fit residues: 78.1628 Evaluate side-chains 237 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.176376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143781 restraints weight = 14251.808| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.38 r_work: 0.3647 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 1.174 Fit side-chains REVERT: C 168 LEU cc_start: 0.7990 (mt) cc_final: 0.7703 (pp) REVERT: C 250 PHE cc_start: 0.8307 (t80) cc_final: 0.7944 (t80) REVERT: H 118 MET cc_start: 0.8089 (mtp) cc_final: 0.7863 (mtt) REVERT: N 99 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7612 (mm-40) outliers start: 39 outliers final: 25 residues processed: 249 average time/residue: 0.1660 time to fit residues: 63.8767 Evaluate side-chains 239 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 214 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 118 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 0.0020 chunk 64 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 overall best weight: 1.0390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.178072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146177 restraints weight = 14264.691| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.43 r_work: 0.3688 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2283 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= 0.184 Angle : 0.549 6.638 14746 Z= 0.288 Chirality : 0.039 0.135 1797 Planarity : 0.004 0.042 1802 Dihedral : 4.035 17.819 1489 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.26 % Allowed : 18.04 % Favored : 78.69 % 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: 0.73 (0.23), residues: 1390 helix: 2.52 (0.18), residues: 666 sheet: -1.12 (0.28), residues: 311 loop : -1.65 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 280 HIS 0.007 0.001 HIS M 58 PHE 0.012 0.001 PHE A 259 TYR 0.013 0.001 TYR H 126 ARG 0.002 0.000 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 278 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 1.202 Fit side-chains REVERT: B 258 LEU cc_start: 0.8374 (mt) cc_final: 0.8077 (mt) REVERT: C 168 LEU cc_start: 0.8001 (mt) cc_final: 0.7681 (pp) REVERT: C 250 PHE cc_start: 0.8321 (t80) cc_final: 0.7965 (t80) REVERT: H 118 MET cc_start: 0.8128 (mtp) cc_final: 0.7892 (mtt) REVERT: M 103 MET cc_start: 0.7450 (mmm) cc_final: 0.7168 (mmm) REVERT: N 99 GLN cc_start: 0.7896 (mm-40) cc_final: 0.6863 (mm-40) outliers start: 34 outliers final: 15 residues processed: 257 average time/residue: 0.1725 time to fit residues: 67.4721 Evaluate side-chains 238 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 223 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL 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 256 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain H residue 28 VAL 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 N residue 25 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 53 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.171959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139535 restraints weight = 14130.287| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.33 r_work: 0.3610 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10777 Z= 0.347 Angle : 0.634 6.798 14746 Z= 0.329 Chirality : 0.042 0.131 1797 Planarity : 0.004 0.047 1802 Dihedral : 4.234 18.171 1489 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.80 % Allowed : 19.19 % Favored : 76.01 % 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: 0.64 (0.23), residues: 1390 helix: 2.40 (0.18), residues: 666 sheet: -1.02 (0.29), residues: 312 loop : -1.74 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 70 HIS 0.007 0.001 HIS H 58 PHE 0.013 0.002 PHE L 107 TYR 0.019 0.002 TYR H 126 ARG 0.002 0.001 ARG O 61 *********************** 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 to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 1.132 Fit side-chains REVERT: C 250 PHE cc_start: 0.8331 (t80) cc_final: 0.7997 (t80) REVERT: C 254 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7482 (tt) REVERT: E 163 LYS cc_start: 0.8690 (tptm) cc_final: 0.8282 (tptp) REVERT: E 176 MET cc_start: 0.8588 (tmm) cc_final: 0.8128 (ttt) REVERT: H 118 MET cc_start: 0.8156 (mtp) cc_final: 0.7921 (mtt) REVERT: N 99 GLN cc_start: 0.7929 (mm-40) cc_final: 0.6966 (mm-40) outliers start: 50 outliers final: 37 residues processed: 256 average time/residue: 0.1772 time to fit residues: 68.9768 Evaluate side-chains 252 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 207 MET Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain B residue 161 SER 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 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 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 267 CYS 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 F residue 161 SER Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 267 CYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain H residue 28 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** E 183 HIS ** 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 = 0.4220 r_free = 0.4220 target = 0.175053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.142650 restraints weight = 14001.635| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.43 r_work: 0.3633 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10777 Z= 0.219 Angle : 0.564 6.755 14746 Z= 0.293 Chirality : 0.040 0.138 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.976 18.040 1489 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.84 % Allowed : 21.21 % 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: 1.00 (0.23), residues: 1390 helix: 2.69 (0.18), residues: 666 sheet: -0.80 (0.30), residues: 307 loop : -1.59 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 280 HIS 0.007 0.001 HIS M 58 PHE 0.015 0.001 PHE A 250 TYR 0.013 0.001 TYR H 126 ARG 0.001 0.000 ARG N 81 *********************** 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 271 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 1.143 Fit side-chains REVERT: C 250 PHE cc_start: 0.8347 (t80) cc_final: 0.8017 (t80) REVERT: E 163 LYS cc_start: 0.8632 (tptm) cc_final: 0.8227 (tptp) REVERT: E 176 MET cc_start: 0.8606 (tmm) cc_final: 0.8120 (ttt) REVERT: H 118 MET cc_start: 0.8069 (mtp) cc_final: 0.7846 (mtt) REVERT: M 103 MET cc_start: 0.7510 (mmm) cc_final: 0.7198 (mmm) REVERT: N 99 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7017 (mm-40) outliers start: 40 outliers final: 27 residues processed: 248 average time/residue: 0.1784 time to fit residues: 67.7549 Evaluate side-chains 244 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 253 LEU 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 253 LEU Chi-restraints excluded: chain C residue 256 LEU 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 F residue 291 ILE Chi-restraints excluded: chain H residue 28 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 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 ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 0.0980 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 71 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.178871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145671 restraints weight = 14279.331| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.31 r_work: 0.3675 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10777 Z= 0.162 Angle : 0.551 6.801 14746 Z= 0.285 Chirality : 0.039 0.179 1797 Planarity : 0.004 0.044 1802 Dihedral : 3.772 17.193 1489 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.36 % Allowed : 21.98 % Favored : 74.66 % 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: 1.28 (0.23), residues: 1390 helix: 2.87 (0.18), residues: 666 sheet: -0.47 (0.29), residues: 303 loop : -1.55 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 280 HIS 0.006 0.001 HIS M 58 PHE 0.015 0.001 PHE E 293 TYR 0.010 0.001 TYR O 126 ARG 0.002 0.000 ARG O 123 *********************** 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 274 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 1.088 Fit side-chains REVERT: A 176 MET cc_start: 0.8600 (tmm) cc_final: 0.8337 (ttt) REVERT: C 250 PHE cc_start: 0.8316 (t80) cc_final: 0.8055 (t80) REVERT: E 163 LYS cc_start: 0.8609 (tptm) cc_final: 0.8217 (tptp) REVERT: E 176 MET cc_start: 0.8572 (tmm) cc_final: 0.8070 (ttt) REVERT: H 125 LYS cc_start: 0.8674 (ptmm) cc_final: 0.8473 (ptmm) REVERT: N 99 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7127 (mm-40) outliers start: 35 outliers final: 25 residues processed: 257 average time/residue: 0.1689 time to fit residues: 67.4996 Evaluate side-chains 247 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 254 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 267 CYS Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain H residue 28 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 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 Chi-restraints excluded: chain P residue 83 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 68 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 134 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.179213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.146248 restraints weight = 14379.838| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.28 r_work: 0.3701 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10777 Z= 0.166 Angle : 0.553 7.893 14746 Z= 0.284 Chirality : 0.039 0.214 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.652 17.206 1489 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.36 % Allowed : 22.65 % 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: 1.45 (0.23), residues: 1390 helix: 2.95 (0.18), residues: 666 sheet: -0.27 (0.30), residues: 300 loop : -1.44 (0.31), residues: 424 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 0.024 0.001 PHE M 52 TYR 0.012 0.001 TYR H 126 ARG 0.003 0.000 ARG N 81 *********************** 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 263 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 1.110 Fit side-chains REVERT: A 176 MET cc_start: 0.8608 (tmm) cc_final: 0.8297 (ttt) REVERT: C 250 PHE cc_start: 0.8290 (t80) cc_final: 0.8047 (t80) REVERT: D 294 MET cc_start: 0.5733 (tpt) cc_final: 0.5209 (tpp) REVERT: E 176 MET cc_start: 0.8559 (tmm) cc_final: 0.8066 (ttt) REVERT: F 290 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6838 (mmm) REVERT: N 99 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7245 (mm-40) REVERT: O 54 THR cc_start: 0.8639 (p) cc_final: 0.8337 (t) outliers start: 35 outliers final: 29 residues processed: 246 average time/residue: 0.1745 time to fit residues: 66.1469 Evaluate side-chains 249 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 253 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 267 CYS Chi-restraints excluded: chain F residue 287 ILE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain H residue 28 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 45 CYS Chi-restraints excluded: chain M residue 95 ILE 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 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 Chi-restraints excluded: chain P residue 83 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 14 optimal weight: 0.0670 chunk 47 optimal weight: 0.0000 chunk 60 optimal weight: 30.0000 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.177512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.145276 restraints weight = 14139.266| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.37 r_work: 0.3669 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10777 Z= 0.216 Angle : 0.581 7.974 14746 Z= 0.296 Chirality : 0.039 0.215 1797 Planarity : 0.004 0.063 1802 Dihedral : 3.699 17.484 1489 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.84 % Allowed : 22.94 % Favored : 73.22 % 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: 1.48 (0.23), residues: 1390 helix: 2.96 (0.18), residues: 666 sheet: -0.24 (0.30), residues: 301 loop : -1.42 (0.31), residues: 423 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 0.031 0.001 PHE O 52 TYR 0.015 0.001 TYR O 55 ARG 0.008 0.001 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 265 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 1.185 Fit side-chains REVERT: A 176 MET cc_start: 0.8610 (tmm) cc_final: 0.8344 (ttt) REVERT: C 250 PHE cc_start: 0.8256 (t80) cc_final: 0.8025 (t80) REVERT: D 193 ILE cc_start: 0.8203 (mp) cc_final: 0.7987 (mp) REVERT: D 294 MET cc_start: 0.5885 (tpt) cc_final: 0.5341 (tpp) REVERT: E 176 MET cc_start: 0.8555 (tmm) cc_final: 0.8092 (ttt) REVERT: F 290 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6874 (mmm) REVERT: N 99 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7250 (mt0) REVERT: O 54 THR cc_start: 0.8688 (p) cc_final: 0.8368 (t) REVERT: P 62 GLN cc_start: 0.7961 (mp10) cc_final: 0.7323 (pt0) outliers start: 40 outliers final: 35 residues processed: 249 average time/residue: 0.1727 time to fit residues: 66.0482 Evaluate side-chains 255 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 253 LEU Chi-restraints excluded: chain A residue 254 LEU 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 177 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain F residue 161 SER 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 F residue 290 MET Chi-restraints excluded: chain H residue 28 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 45 CYS Chi-restraints excluded: chain M residue 95 ILE 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 Chi-restraints excluded: chain P residue 83 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.174184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141189 restraints weight = 14406.541| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.38 r_work: 0.3615 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 10777 Z= 0.298 Angle : 0.631 8.814 14746 Z= 0.321 Chirality : 0.041 0.291 1797 Planarity : 0.004 0.046 1802 Dihedral : 3.885 18.091 1489 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.13 % Allowed : 23.22 % Favored : 72.65 % 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: 1.27 (0.23), residues: 1390 helix: 2.80 (0.18), residues: 666 sheet: -0.45 (0.30), residues: 310 loop : -1.49 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 70 HIS 0.006 0.001 HIS H 58 PHE 0.019 0.002 PHE O 52 TYR 0.015 0.002 TYR H 126 ARG 0.005 0.001 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 260 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 1.275 Fit side-chains REVERT: A 176 MET cc_start: 0.8647 (tmm) cc_final: 0.8426 (ttt) REVERT: C 250 PHE cc_start: 0.8284 (t80) cc_final: 0.8040 (t80) REVERT: D 294 MET cc_start: 0.5833 (tpt) cc_final: 0.5260 (tpp) REVERT: E 163 LYS cc_start: 0.8641 (tptm) cc_final: 0.8319 (tptp) REVERT: E 176 MET cc_start: 0.8583 (tmm) cc_final: 0.8349 (ttt) REVERT: L 62 GLN cc_start: 0.7971 (mp10) cc_final: 0.7197 (pt0) REVERT: N 99 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7264 (mm-40) REVERT: P 62 GLN cc_start: 0.7990 (mp10) cc_final: 0.7277 (pt0) outliers start: 43 outliers final: 36 residues processed: 245 average time/residue: 0.1591 time to fit residues: 60.8136 Evaluate side-chains 249 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 253 LEU 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 214 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 287 ILE 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 E residue 177 VAL Chi-restraints excluded: chain E residue 261 LEU 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 287 ILE Chi-restraints excluded: chain H residue 28 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 45 CYS Chi-restraints excluded: chain M residue 95 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 69 optimal weight: 0.0570 chunk 63 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.178665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.145191 restraints weight = 14228.306| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.46 r_work: 0.3671 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10777 Z= 0.180 Angle : 0.595 10.718 14746 Z= 0.297 Chirality : 0.040 0.349 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.694 17.680 1489 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.88 % Allowed : 24.76 % Favored : 72.36 % 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: 1.55 (0.23), residues: 1390 helix: 3.04 (0.18), residues: 666 sheet: -0.20 (0.30), residues: 304 loop : -1.44 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 280 HIS 0.006 0.001 HIS M 58 PHE 0.030 0.001 PHE O 52 TYR 0.013 0.001 TYR H 126 ARG 0.007 0.000 ARG O 123 ********************** 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 256 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 1.072 Fit side-chains REVERT: A 176 MET cc_start: 0.8626 (tmm) cc_final: 0.8328 (ttt) REVERT: C 163 LYS cc_start: 0.8706 (tptt) cc_final: 0.8503 (tptp) REVERT: D 294 MET cc_start: 0.5732 (tpt) cc_final: 0.5142 (tpp) REVERT: E 163 LYS cc_start: 0.8619 (tptm) cc_final: 0.8303 (tptp) REVERT: E 176 MET cc_start: 0.8569 (tmm) cc_final: 0.8124 (ttt) REVERT: L 62 GLN cc_start: 0.7823 (mp10) cc_final: 0.7141 (pt0) REVERT: N 62 GLN cc_start: 0.8068 (mp10) cc_final: 0.7306 (pt0) REVERT: N 99 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7228 (mt0) REVERT: P 62 GLN cc_start: 0.7828 (mp10) cc_final: 0.7276 (pt0) outliers start: 30 outliers final: 28 residues processed: 245 average time/residue: 0.1662 time to fit residues: 63.0007 Evaluate side-chains 251 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 253 LEU 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 287 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 161 SER 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 28 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 95 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 8.9990 chunk 111 optimal weight: 0.0000 chunk 110 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 12 optimal weight: 40.0000 chunk 11 optimal weight: 6.9990 chunk 94 optimal weight: 0.2980 chunk 101 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.178826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.145194 restraints weight = 14183.289| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.46 r_work: 0.3688 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10777 Z= 0.184 Angle : 0.596 11.453 14746 Z= 0.296 Chirality : 0.040 0.315 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.650 17.285 1489 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.07 % Allowed : 25.05 % Favored : 71.88 % 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: 1.61 (0.23), residues: 1390 helix: 3.07 (0.18), residues: 666 sheet: -0.15 (0.30), residues: 304 loop : -1.41 (0.31), residues: 420 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 0.025 0.001 PHE O 52 TYR 0.012 0.001 TYR H 126 ARG 0.006 0.000 ARG O 123 =============================================================================== Job complete usr+sys time: 5063.37 seconds wall clock time: 90 minutes 37.59 seconds (5437.59 seconds total)