Starting phenix.real_space_refine on Mon Jul 28 16:36:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kr5_23002/07_2025/7kr5_23002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kr5_23002/07_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_23002/07_2025/7kr5_23002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kr5_23002/07_2025/7kr5_23002.map" model { file = "/net/cci-nas-00/data/ceres_data/7kr5_23002/07_2025/7kr5_23002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kr5_23002/07_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-5711/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: 6.68, per 1000 atoms: 0.63 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 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: 1.21 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: 3.40 Time building geometry restraints manager: 3.37 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: 1.040 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.630 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.820 ------------------------------------------------------------------------------- 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 10782 Z= 0.193 Angle : 0.566 6.218 14756 Z= 0.308 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 Details of bonding type rmsd hydrogen bonds : bond 0.10488 ( 717) hydrogen bonds : angle 5.34996 ( 2097) SS BOND : bond 0.00190 ( 5) SS BOND : angle 0.49414 ( 10) covalent geometry : bond 0.00390 (10777) covalent geometry : angle 0.56595 (14746) *********************** 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 : 1.099 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: 0.1597 time to fit residues: 75.5081 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 : 1.017 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.173895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141668 restraints weight = 14180.347| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.36 r_work: 0.3645 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 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 = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10782 Z= 0.229 Angle : 0.647 7.077 14756 Z= 0.342 Chirality : 0.043 0.145 1797 Planarity : 0.004 0.042 1802 Dihedral : 4.587 27.614 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 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 717) hydrogen bonds : angle 4.56218 ( 2097) SS BOND : bond 0.00493 ( 5) SS BOND : angle 0.80632 ( 10) covalent geometry : bond 0.00531 (10777) covalent geometry : angle 0.64736 (14746) *********************** 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 : 1.154 Fit side-chains REVERT: C 168 LEU cc_start: 0.7993 (mt) cc_final: 0.7702 (pp) REVERT: C 250 PHE cc_start: 0.8311 (t80) cc_final: 0.7948 (t80) REVERT: H 118 MET cc_start: 0.8084 (mtp) cc_final: 0.7858 (mtt) REVERT: N 99 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7616 (mm-40) outliers start: 39 outliers final: 25 residues processed: 249 average time/residue: 0.1690 time to fit residues: 64.8963 Evaluate side-chains 238 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 0.0000 chunk 64 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.176212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.144029 restraints weight = 14276.921| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.46 r_work: 0.3666 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10782 Z= 0.159 Angle : 0.568 6.650 14756 Z= 0.298 Chirality : 0.040 0.140 1797 Planarity : 0.004 0.043 1802 Dihedral : 4.122 18.118 1489 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.61 % Allowed : 17.27 % Favored : 78.12 % 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: 0.62 (0.23), residues: 1390 helix: 2.44 (0.18), residues: 666 sheet: -1.19 (0.28), residues: 314 loop : -1.69 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 70 HIS 0.007 0.001 HIS H 58 PHE 0.011 0.001 PHE A 259 TYR 0.015 0.001 TYR H 126 ARG 0.002 0.001 ARG P 74 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 717) hydrogen bonds : angle 4.30971 ( 2097) SS BOND : bond 0.00364 ( 5) SS BOND : angle 0.33418 ( 10) covalent geometry : bond 0.00349 (10777) covalent geometry : angle 0.56791 (14746) *********************** 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 290 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 1.077 Fit side-chains REVERT: C 168 LEU cc_start: 0.8034 (mt) cc_final: 0.7629 (pp) REVERT: C 176 MET cc_start: 0.8549 (tmm) cc_final: 0.8235 (ttt) REVERT: C 250 PHE cc_start: 0.8321 (t80) cc_final: 0.7974 (t80) REVERT: E 163 LYS cc_start: 0.8694 (tptm) cc_final: 0.8264 (tptp) REVERT: H 118 MET cc_start: 0.8139 (mtp) cc_final: 0.7896 (mtt) REVERT: M 103 MET cc_start: 0.7445 (mmm) cc_final: 0.7107 (mmm) REVERT: N 99 GLN cc_start: 0.7921 (mm-40) cc_final: 0.6875 (mm-40) outliers start: 48 outliers final: 25 residues processed: 263 average time/residue: 0.1684 time to fit residues: 67.8835 Evaluate side-chains 250 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain 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 41 LEU Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 53 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 = 0.4187 r_free = 0.4187 target = 0.171642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.139912 restraints weight = 14153.360| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.25 r_work: 0.3605 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10782 Z= 0.230 Angle : 0.642 6.817 14756 Z= 0.332 Chirality : 0.042 0.132 1797 Planarity : 0.004 0.046 1802 Dihedral : 4.266 18.376 1489 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.09 % Allowed : 18.91 % 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: 0.60 (0.23), residues: 1390 helix: 2.40 (0.18), residues: 666 sheet: -1.05 (0.29), residues: 312 loop : -1.81 (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 0.012 0.002 PHE M 52 TYR 0.018 0.002 TYR H 126 ARG 0.003 0.001 ARG P 74 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 717) hydrogen bonds : angle 4.42541 ( 2097) SS BOND : bond 0.00268 ( 5) SS BOND : angle 0.51538 ( 10) covalent geometry : bond 0.00543 (10777) covalent geometry : angle 0.64216 (14746) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 1.147 Fit side-chains REVERT: A 176 MET cc_start: 0.8752 (tmm) cc_final: 0.8427 (ttt) REVERT: C 250 PHE cc_start: 0.8282 (t80) cc_final: 0.7956 (t80) REVERT: E 163 LYS cc_start: 0.8723 (tptm) cc_final: 0.8311 (tptp) REVERT: E 176 MET cc_start: 0.8610 (tmm) cc_final: 0.8145 (ttt) REVERT: H 118 MET cc_start: 0.8152 (mtp) cc_final: 0.7903 (mtt) REVERT: M 54 THR cc_start: 0.8533 (p) cc_final: 0.8331 (t) REVERT: N 99 GLN cc_start: 0.7895 (mm-40) cc_final: 0.6880 (mm-40) outliers start: 53 outliers final: 40 residues processed: 255 average time/residue: 0.2021 time to fit residues: 78.8808 Evaluate side-chains 252 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 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 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 211 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 197 ILE 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 41 LEU 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 106 LEU 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: 1.9990 chunk 66 optimal weight: 0.0770 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.173467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.140952 restraints weight = 14039.286| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.50 r_work: 0.3597 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10782 Z= 0.169 Angle : 0.581 6.766 14756 Z= 0.301 Chirality : 0.041 0.154 1797 Planarity : 0.004 0.045 1802 Dihedral : 4.057 18.230 1489 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.51 % Allowed : 20.73 % Favored : 74.76 % 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: 0.88 (0.23), residues: 1390 helix: 2.62 (0.18), residues: 666 sheet: -0.89 (0.30), residues: 308 loop : -1.68 (0.31), residues: 416 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 0.010 0.001 PHE A 259 TYR 0.014 0.002 TYR H 126 ARG 0.002 0.000 ARG H 73 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 717) hydrogen bonds : angle 4.24734 ( 2097) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.31017 ( 10) covalent geometry : bond 0.00387 (10777) covalent geometry : angle 0.58068 (14746) *********************** 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 276 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 229 time to evaluate : 1.913 Fit side-chains REVERT: C 250 PHE cc_start: 0.8292 (t80) cc_final: 0.7973 (t80) REVERT: C 294 MET cc_start: 0.8728 (tpt) cc_final: 0.8514 (tpt) REVERT: E 163 LYS cc_start: 0.8708 (tptm) cc_final: 0.8315 (tptp) REVERT: E 176 MET cc_start: 0.8617 (tmm) cc_final: 0.8311 (ttt) REVERT: H 118 MET cc_start: 0.8130 (mtp) cc_final: 0.7889 (mtt) REVERT: M 103 MET cc_start: 0.7515 (mmm) cc_final: 0.7212 (mmm) REVERT: N 99 GLN cc_start: 0.7868 (mm-40) cc_final: 0.6934 (mm-40) outliers start: 47 outliers final: 35 residues processed: 256 average time/residue: 0.2620 time to fit residues: 102.9519 Evaluate side-chains 249 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 3.850 ------------------------------------------------------------------------------- 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 161 SER 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 210 LEU 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 161 SER Chi-restraints excluded: chain D residue 257 ILE 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 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 106 LEU 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: 0.0570 chunk 118 optimal weight: 0.9980 chunk 131 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.178505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145678 restraints weight = 14307.577| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.33 r_work: 0.3669 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 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 = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.130 | | 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: 0.7781 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10782 Z= 0.122 Angle : 0.557 6.821 14756 Z= 0.287 Chirality : 0.039 0.180 1797 Planarity : 0.004 0.044 1802 Dihedral : 3.820 17.239 1489 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.36 % Allowed : 22.46 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.23), residues: 1390 helix: 2.86 (0.18), residues: 666 sheet: -0.52 (0.29), residues: 303 loop : -1.64 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 280 HIS 0.006 0.001 HIS M 58 PHE 0.010 0.001 PHE A 259 TYR 0.010 0.001 TYR H 126 ARG 0.002 0.000 ARG O 123 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 717) hydrogen bonds : angle 4.05867 ( 2097) SS BOND : bond 0.00206 ( 5) SS BOND : angle 0.42285 ( 10) covalent geometry : bond 0.00249 (10777) covalent geometry : angle 0.55739 (14746) *********************** 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 273 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 1.834 Fit side-chains REVERT: C 250 PHE cc_start: 0.8332 (t80) cc_final: 0.8032 (t80) REVERT: E 163 LYS cc_start: 0.8631 (tptm) cc_final: 0.8232 (tptp) REVERT: E 176 MET cc_start: 0.8591 (tmm) cc_final: 0.8112 (ttt) REVERT: H 118 MET cc_start: 0.8066 (mtp) cc_final: 0.7863 (mtt) REVERT: N 99 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7096 (mm-40) outliers start: 35 outliers final: 22 residues processed: 252 average time/residue: 0.2144 time to fit residues: 83.7630 Evaluate side-chains 242 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 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 E residue 177 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 0.0050 chunk 68 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 111 optimal weight: 9.9990 chunk 134 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 101 optimal weight: 0.0020 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.180079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147502 restraints weight = 14275.531| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.26 r_work: 0.3719 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10782 Z= 0.115 Angle : 0.555 8.012 14756 Z= 0.282 Chirality : 0.038 0.163 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.639 16.977 1489 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.98 % Allowed : 23.32 % Favored : 73.70 % 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: 1.50 (0.23), residues: 1390 helix: 3.00 (0.18), residues: 666 sheet: -0.21 (0.31), residues: 289 loop : -1.44 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 280 HIS 0.005 0.001 HIS M 58 PHE 0.010 0.001 PHE A 259 TYR 0.010 0.001 TYR H 126 ARG 0.002 0.000 ARG O 123 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 717) hydrogen bonds : angle 3.95043 ( 2097) SS BOND : bond 0.00217 ( 5) SS BOND : angle 0.44323 ( 10) covalent geometry : bond 0.00235 (10777) covalent geometry : angle 0.55519 (14746) *********************** 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 267 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 1.050 Fit side-chains REVERT: C 250 PHE cc_start: 0.8281 (t80) cc_final: 0.7999 (t80) REVERT: E 176 MET cc_start: 0.8532 (tmm) cc_final: 0.8042 (ttt) REVERT: F 290 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6835 (mmm) REVERT: N 99 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7153 (mm-40) outliers start: 31 outliers final: 24 residues processed: 253 average time/residue: 0.1703 time to fit residues: 65.2503 Evaluate side-chains 246 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET 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 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 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: 2.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 14 optimal weight: 0.0270 chunk 47 optimal weight: 7.9990 chunk 60 optimal weight: 40.0000 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.175334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.144086 restraints weight = 14186.536| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.30 r_work: 0.3626 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10782 Z= 0.174 Angle : 0.607 8.147 14756 Z= 0.310 Chirality : 0.040 0.240 1797 Planarity : 0.004 0.065 1802 Dihedral : 3.800 17.595 1489 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.55 % Allowed : 23.99 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1390 helix: 2.87 (0.18), residues: 666 sheet: -0.35 (0.30), residues: 304 loop : -1.45 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 268 HIS 0.006 0.001 HIS M 58 PHE 0.030 0.001 PHE O 52 TYR 0.018 0.002 TYR O 55 ARG 0.008 0.001 ARG O 123 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 717) hydrogen bonds : angle 4.12707 ( 2097) SS BOND : bond 0.00289 ( 5) SS BOND : angle 0.51398 ( 10) covalent geometry : bond 0.00408 (10777) covalent geometry : angle 0.60666 (14746) *********************** 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 256 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 1.242 Fit side-chains REVERT: B 292 ILE cc_start: 0.6663 (mt) cc_final: 0.6392 (mt) REVERT: C 250 PHE cc_start: 0.8285 (t80) cc_final: 0.8013 (t80) REVERT: D 294 MET cc_start: 0.5813 (tpt) cc_final: 0.5230 (tpp) REVERT: E 176 MET cc_start: 0.8543 (tmm) cc_final: 0.8295 (ttt) REVERT: N 99 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7160 (mm-40) REVERT: P 62 GLN cc_start: 0.7988 (mp10) cc_final: 0.7299 (pt0) outliers start: 37 outliers final: 29 residues processed: 238 average time/residue: 0.2066 time to fit residues: 74.7692 Evaluate side-chains 243 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 273 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.178165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145940 restraints weight = 14336.292| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.41 r_work: 0.3648 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10782 Z= 0.127 Angle : 0.580 8.866 14756 Z= 0.291 Chirality : 0.039 0.245 1797 Planarity : 0.004 0.046 1802 Dihedral : 3.670 17.581 1489 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 1.54 (0.23), residues: 1390 helix: 3.02 (0.18), residues: 666 sheet: -0.22 (0.30), residues: 304 loop : -1.40 (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 0.028 0.001 PHE O 52 TYR 0.011 0.001 TYR O 126 ARG 0.007 0.000 ARG O 123 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 717) hydrogen bonds : angle 3.99596 ( 2097) SS BOND : bond 0.00208 ( 5) SS BOND : angle 0.40583 ( 10) covalent geometry : bond 0.00280 (10777) covalent geometry : angle 0.58040 (14746) *********************** 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 253 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 1.180 Fit side-chains REVERT: B 294 MET cc_start: 0.5838 (tpt) cc_final: 0.5504 (tpt) REVERT: C 250 PHE cc_start: 0.8250 (t80) cc_final: 0.8004 (t80) REVERT: D 294 MET cc_start: 0.5843 (tpt) cc_final: 0.5240 (tpp) REVERT: E 163 LYS cc_start: 0.8630 (tptm) cc_final: 0.8312 (tptp) REVERT: E 176 MET cc_start: 0.8533 (tmm) cc_final: 0.8097 (ttt) REVERT: F 290 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6869 (mmm) REVERT: L 62 GLN cc_start: 0.7851 (mp10) cc_final: 0.7120 (pt0) REVERT: N 62 GLN cc_start: 0.7979 (mp10) cc_final: 0.7389 (pt0) REVERT: N 99 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7207 (mt0) REVERT: P 62 GLN cc_start: 0.7912 (mp10) cc_final: 0.7305 (pt0) outliers start: 30 outliers final: 23 residues processed: 238 average time/residue: 0.1748 time to fit residues: 64.2787 Evaluate side-chains 242 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 69 optimal weight: 0.0770 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.0020 chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.4546 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.176781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.142644 restraints weight = 14359.989| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.42 r_work: 0.3718 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10782 Z= 0.118 Angle : 0.593 10.525 14756 Z= 0.292 Chirality : 0.039 0.245 1797 Planarity : 0.004 0.046 1802 Dihedral : 3.560 16.974 1489 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.78 % Allowed : 25.43 % Favored : 71.79 % 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: 1.67 (0.23), residues: 1390 helix: 3.14 (0.18), residues: 666 sheet: -0.13 (0.31), residues: 298 loop : -1.38 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 280 HIS 0.005 0.001 HIS M 58 PHE 0.029 0.001 PHE O 52 TYR 0.011 0.001 TYR O 126 ARG 0.006 0.000 ARG O 123 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 717) hydrogen bonds : angle 3.90669 ( 2097) SS BOND : bond 0.00240 ( 5) SS BOND : angle 0.52371 ( 10) covalent geometry : bond 0.00255 (10777) covalent geometry : angle 0.59312 (14746) ********************** 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 254 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 1.073 Fit side-chains REVERT: D 294 MET cc_start: 0.5620 (tpt) cc_final: 0.5002 (tpp) REVERT: E 163 LYS cc_start: 0.8610 (tptm) cc_final: 0.8309 (tptp) REVERT: L 62 GLN cc_start: 0.7850 (mp10) cc_final: 0.7200 (pt0) REVERT: L 99 GLN cc_start: 0.7615 (mm-40) cc_final: 0.6838 (mt0) REVERT: N 62 GLN cc_start: 0.7909 (mp10) cc_final: 0.7339 (pt0) REVERT: N 99 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7237 (mt0) REVERT: P 62 GLN cc_start: 0.7809 (mp10) cc_final: 0.7300 (pt0) REVERT: P 99 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7407 (mt0) outliers start: 29 outliers final: 23 residues processed: 237 average time/residue: 0.1805 time to fit residues: 65.0820 Evaluate side-chains 243 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 273 ASP 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 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 103 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.0670 chunk 111 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 98 optimal weight: 0.0970 chunk 86 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 40.0000 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 101 optimal weight: 0.0980 chunk 129 optimal weight: 0.3980 overall best weight: 0.1454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.183162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.149388 restraints weight = 14191.962| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.50 r_work: 0.3755 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10782 Z= 0.114 Angle : 0.575 10.788 14756 Z= 0.284 Chirality : 0.038 0.218 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.508 16.589 1489 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.40 % Allowed : 26.01 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.23), residues: 1390 helix: 3.29 (0.18), residues: 666 sheet: -0.09 (0.31), residues: 295 loop : -1.26 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 268 HIS 0.005 0.001 HIS H 58 PHE 0.030 0.001 PHE O 52 TYR 0.009 0.001 TYR N 56 ARG 0.003 0.000 ARG O 123 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 717) hydrogen bonds : angle 3.80955 ( 2097) SS BOND : bond 0.00220 ( 5) SS BOND : angle 0.48462 ( 10) covalent geometry : bond 0.00238 (10777) covalent geometry : angle 0.57554 (14746) =============================================================================== Job complete usr+sys time: 6142.14 seconds wall clock time: 112 minutes 28.55 seconds (6748.55 seconds total)