Starting phenix.real_space_refine on Wed Mar 4 03:30:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kr5_23002/03_2026/7kr5_23002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kr5_23002/03_2026/7kr5_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_23002/03_2026/7kr5_23002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kr5_23002/03_2026/7kr5_23002.map" model { file = "/net/cci-nas-00/data/ceres_data/7kr5_23002/03_2026/7kr5_23002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kr5_23002/03_2026/7kr5_23002.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 4, 'ARG:plan': 1} 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, 'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 4, 'ARG:plan': 1} 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, 'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 4, 'ARG:plan': 1} 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: 2.56, per 1000 atoms: 0.24 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: 0.76 Conformation dependent library (CDL) restraints added in 547.5 milliseconds 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: 0.20 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: 1.81 Time building geometry restraints manager: 1.06 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: 1.820 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.010 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.790 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.001 ARG M 92 TYR 0.008 0.002 TYR N 73 PHE 0.007 0.001 PHE L 82 TRP 0.009 0.001 TRP H 70 HIS 0.004 0.001 HIS D 299 Details of bonding type rmsd covalent geometry : bond 0.00390 (10777) covalent geometry : angle 0.56595 (14746) SS BOND : bond 0.00190 ( 5) SS BOND : angle 0.49414 ( 10) hydrogen bonds : bond 0.10488 ( 717) hydrogen bonds : angle 5.34996 ( 2097) *********************** 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 : 0.330 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: 0.8339 (ptmm) REVERT: M 103 MET cc_start: 0.8161 (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: 0.7366 (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: 0.0655 time to fit residues: 31.8115 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 : 0.425 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 M 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.182057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.146930 restraints weight = 14134.945| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.16 r_work: 0.3761 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10782 Z= 0.134 Angle : 0.567 6.580 14756 Z= 0.298 Chirality : 0.039 0.139 1797 Planarity : 0.004 0.044 1802 Dihedral : 4.290 31.707 1492 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.69 % Allowed : 14.97 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1390 helix: 2.34 (0.19), residues: 666 sheet: -1.11 (0.28), residues: 289 loop : -1.77 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 81 TYR 0.015 0.001 TYR H 126 PHE 0.015 0.001 PHE E 259 TRP 0.012 0.001 TRP M 70 HIS 0.006 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00274 (10777) covalent geometry : angle 0.56698 (14746) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.73904 ( 10) hydrogen bonds : bond 0.04444 ( 717) hydrogen bonds : angle 4.36299 ( 2097) *********************** 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 281 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.439 Fit side-chains REVERT: B 193 ILE cc_start: 0.8618 (mt) cc_final: 0.8243 (mt) REVERT: B 211 MET cc_start: 0.7511 (tmm) cc_final: 0.7252 (tmm) REVERT: C 211 MET cc_start: 0.8118 (ttp) cc_final: 0.7898 (ttp) REVERT: C 250 PHE cc_start: 0.8307 (t80) cc_final: 0.7910 (t80) REVERT: E 268 TRP cc_start: 0.8188 (t-100) cc_final: 0.7945 (t-100) REVERT: N 99 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7569 (mm-40) REVERT: P 125 GLU cc_start: 0.6867 (tp30) cc_final: 0.6436 (tm-30) outliers start: 28 outliers final: 11 residues processed: 263 average time/residue: 0.0615 time to fit residues: 25.8250 Evaluate side-chains 240 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain M residue 28 VAL 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 126 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 62 optimal weight: 0.0010 chunk 6 optimal weight: 7.9990 chunk 92 optimal weight: 0.0270 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 overall best weight: 0.7846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.181152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.148584 restraints weight = 14081.556| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.17 r_work: 0.3731 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3739 r_free = 0.3739 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10782 Z= 0.124 Angle : 0.540 9.541 14756 Z= 0.279 Chirality : 0.039 0.132 1797 Planarity : 0.004 0.043 1802 Dihedral : 3.881 17.516 1489 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.69 % Allowed : 17.66 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.23), residues: 1390 helix: 2.66 (0.18), residues: 666 sheet: -0.70 (0.29), residues: 274 loop : -1.68 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 81 TYR 0.014 0.001 TYR H 126 PHE 0.011 0.001 PHE D 171 TRP 0.008 0.001 TRP E 248 HIS 0.005 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00256 (10777) covalent geometry : angle 0.54025 (14746) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.30371 ( 10) hydrogen bonds : bond 0.04132 ( 717) hydrogen bonds : angle 4.11938 ( 2097) *********************** 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 270 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 0.387 Fit side-chains REVERT: B 193 ILE cc_start: 0.8697 (mt) cc_final: 0.8335 (mt) REVERT: C 250 PHE cc_start: 0.8274 (t80) cc_final: 0.7883 (t80) REVERT: N 99 GLN cc_start: 0.7899 (mm-40) cc_final: 0.6936 (mm-40) outliers start: 28 outliers final: 17 residues processed: 251 average time/residue: 0.0646 time to fit residues: 25.6429 Evaluate side-chains 237 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain B residue 267 CYS Chi-restraints excluded: chain C residue 167 LEU 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 F residue 291 ILE Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 120 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 17 optimal weight: 0.0770 chunk 106 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.179985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146868 restraints weight = 14108.750| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.19 r_work: 0.3724 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2527 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= 0.131 Angle : 0.547 8.253 14756 Z= 0.282 Chirality : 0.038 0.130 1797 Planarity : 0.004 0.044 1802 Dihedral : 3.815 17.660 1489 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.17 % Allowed : 17.95 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1390 helix: 2.83 (0.18), residues: 666 sheet: -0.60 (0.30), residues: 268 loop : -1.62 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 81 TYR 0.023 0.001 TYR O 85 PHE 0.009 0.001 PHE D 171 TRP 0.008 0.001 TRP E 248 HIS 0.005 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00280 (10777) covalent geometry : angle 0.54687 (14746) SS BOND : bond 0.00388 ( 5) SS BOND : angle 0.68215 ( 10) hydrogen bonds : bond 0.04036 ( 717) hydrogen bonds : angle 4.03448 ( 2097) *********************** 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 261 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 0.256 Fit side-chains REVERT: B 193 ILE cc_start: 0.8720 (mt) cc_final: 0.8344 (mt) REVERT: C 176 MET cc_start: 0.8489 (tmm) cc_final: 0.8225 (ttt) REVERT: C 250 PHE cc_start: 0.8259 (t80) cc_final: 0.7908 (t80) REVERT: L 80 ASP cc_start: 0.7931 (t0) cc_final: 0.7686 (t0) REVERT: N 99 GLN cc_start: 0.7831 (mm-40) cc_final: 0.6992 (mm-40) REVERT: P 125 GLU cc_start: 0.6759 (tp30) cc_final: 0.6315 (tm-30) outliers start: 33 outliers final: 22 residues processed: 245 average time/residue: 0.0671 time to fit residues: 25.8098 Evaluate side-chains 240 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 263 ILE 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 267 CYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain H residue 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 12 optimal weight: 40.0000 chunk 53 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 48 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.171859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140000 restraints weight = 14235.470| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.41 r_work: 0.3583 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10782 Z= 0.265 Angle : 0.677 7.411 14756 Z= 0.348 Chirality : 0.043 0.154 1797 Planarity : 0.004 0.049 1802 Dihedral : 4.185 18.552 1489 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.51 % Allowed : 18.33 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.23), residues: 1390 helix: 2.54 (0.18), residues: 666 sheet: -1.12 (0.29), residues: 318 loop : -1.59 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 73 TYR 0.019 0.002 TYR H 126 PHE 0.016 0.002 PHE D 171 TRP 0.014 0.002 TRP M 70 HIS 0.008 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00626 (10777) covalent geometry : angle 0.67683 (14746) SS BOND : bond 0.00285 ( 5) SS BOND : angle 0.56408 ( 10) hydrogen bonds : bond 0.04628 ( 717) hydrogen bonds : angle 4.38807 ( 2097) *********************** 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 269 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: C 250 PHE cc_start: 0.8283 (t80) cc_final: 0.7950 (t80) REVERT: E 176 MET cc_start: 0.8587 (tmm) cc_final: 0.8224 (ttt) REVERT: L 80 ASP cc_start: 0.8100 (t0) cc_final: 0.7817 (t0) REVERT: N 99 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7055 (mm-40) outliers start: 47 outliers final: 39 residues processed: 251 average time/residue: 0.0676 time to fit residues: 26.5722 Evaluate side-chains 247 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 287 ILE 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 B residue 273 ASP 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 C residue 285 VAL 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 257 ILE Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 267 CYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 126 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 0.0060 chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.178890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145132 restraints weight = 14183.464| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.29 r_work: 0.3708 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 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 = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3026 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= 0.116 Angle : 0.545 7.066 14756 Z= 0.281 Chirality : 0.038 0.147 1797 Planarity : 0.004 0.044 1802 Dihedral : 3.810 17.773 1489 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.88 % Allowed : 20.44 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.23), residues: 1390 helix: 2.98 (0.18), residues: 666 sheet: -0.63 (0.30), residues: 301 loop : -1.62 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 123 TYR 0.011 0.001 TYR M 126 PHE 0.012 0.001 PHE C 259 TRP 0.010 0.001 TRP F 280 HIS 0.007 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00235 (10777) covalent geometry : angle 0.54565 (14746) SS BOND : bond 0.00193 ( 5) SS BOND : angle 0.24798 ( 10) hydrogen bonds : bond 0.03967 ( 717) hydrogen bonds : angle 4.00811 ( 2097) *********************** 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 264 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.323 Fit side-chains REVERT: C 250 PHE cc_start: 0.8229 (t80) cc_final: 0.7907 (t80) REVERT: E 163 LYS cc_start: 0.8583 (tptm) cc_final: 0.8210 (tptp) REVERT: E 176 MET cc_start: 0.8565 (tmm) cc_final: 0.8086 (ttt) REVERT: L 80 ASP cc_start: 0.7898 (t0) cc_final: 0.7636 (t0) REVERT: N 99 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7056 (mm-40) outliers start: 30 outliers final: 23 residues processed: 249 average time/residue: 0.0663 time to fit residues: 26.1519 Evaluate side-chains 245 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 258 LEU 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 116 THR Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 83 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 100 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.174829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.142368 restraints weight = 14312.787| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.39 r_work: 0.3632 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 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 = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10782 Z= 0.191 Angle : 0.608 7.800 14756 Z= 0.311 Chirality : 0.040 0.134 1797 Planarity : 0.004 0.047 1802 Dihedral : 3.893 17.649 1489 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.03 % Allowed : 21.50 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.23), residues: 1390 helix: 2.79 (0.18), residues: 666 sheet: -0.82 (0.30), residues: 312 loop : -1.56 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 73 TYR 0.016 0.002 TYR H 126 PHE 0.017 0.002 PHE E 250 TRP 0.009 0.001 TRP H 70 HIS 0.008 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00450 (10777) covalent geometry : angle 0.60837 (14746) SS BOND : bond 0.00261 ( 5) SS BOND : angle 0.39962 ( 10) hydrogen bonds : bond 0.04216 ( 717) hydrogen bonds : angle 4.16331 ( 2097) *********************** 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 255 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: C 250 PHE cc_start: 0.8286 (t80) cc_final: 0.7976 (t80) REVERT: E 163 LYS cc_start: 0.8572 (tptm) cc_final: 0.8211 (tptp) REVERT: E 176 MET cc_start: 0.8599 (tmm) cc_final: 0.8267 (ttt) REVERT: L 80 ASP cc_start: 0.7972 (t0) cc_final: 0.7709 (t0) REVERT: N 99 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7151 (mm-40) outliers start: 42 outliers final: 32 residues processed: 239 average time/residue: 0.0671 time to fit residues: 25.2572 Evaluate side-chains 240 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 ILE 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 B residue 273 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 116 THR Chi-restraints excluded: chain P residue 25 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 92 optimal weight: 0.0870 chunk 12 optimal weight: 40.0000 chunk 71 optimal weight: 7.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.178122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143855 restraints weight = 14136.531| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.39 r_work: 0.3696 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3268 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= 0.126 Angle : 0.569 8.842 14756 Z= 0.287 Chirality : 0.038 0.174 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.735 17.932 1489 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.55 % Allowed : 22.36 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.23), residues: 1390 helix: 2.96 (0.18), residues: 666 sheet: -0.46 (0.30), residues: 297 loop : -1.57 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 123 TYR 0.012 0.001 TYR O 126 PHE 0.009 0.001 PHE A 250 TRP 0.009 0.001 TRP F 280 HIS 0.007 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00278 (10777) covalent geometry : angle 0.56911 (14746) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.22699 ( 10) hydrogen bonds : bond 0.03911 ( 717) hydrogen bonds : angle 4.00282 ( 2097) *********************** 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 : 0.334 Fit side-chains revert: symmetry clash REVERT: C 250 PHE cc_start: 0.8223 (t80) cc_final: 0.7930 (t80) REVERT: D 294 MET cc_start: 0.5763 (tpt) cc_final: 0.5189 (tpp) REVERT: E 163 LYS cc_start: 0.8597 (tptm) cc_final: 0.8235 (tptp) REVERT: E 176 MET cc_start: 0.8557 (tmm) cc_final: 0.8180 (ttt) REVERT: L 80 ASP cc_start: 0.7872 (t0) cc_final: 0.7635 (t0) REVERT: N 99 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7189 (mm-40) REVERT: O 54 THR cc_start: 0.8663 (p) cc_final: 0.8328 (t) outliers start: 37 outliers final: 31 residues processed: 241 average time/residue: 0.0666 time to fit residues: 25.4984 Evaluate side-chains 245 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 285 VAL 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 H residue 28 VAL Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 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 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 55 optimal weight: 9.9990 chunk 60 optimal weight: 40.0000 chunk 99 optimal weight: 3.9990 chunk 126 optimal weight: 0.0030 chunk 90 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 48 optimal weight: 30.0000 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.4264 r_free = 0.4264 target = 0.178935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145322 restraints weight = 14103.745| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.26 r_work: 0.3705 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3702 r_free = 0.3702 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10782 Z= 0.122 Angle : 0.574 9.090 14756 Z= 0.286 Chirality : 0.038 0.156 1797 Planarity : 0.004 0.045 1802 Dihedral : 3.626 17.301 1489 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.36 % Allowed : 22.65 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.23), residues: 1390 helix: 3.02 (0.18), residues: 666 sheet: -0.33 (0.31), residues: 294 loop : -1.44 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 123 TYR 0.012 0.001 TYR H 126 PHE 0.009 0.001 PHE A 250 TRP 0.008 0.001 TRP F 280 HIS 0.006 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00266 (10777) covalent geometry : angle 0.57385 (14746) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.25370 ( 10) hydrogen bonds : bond 0.03811 ( 717) hydrogen bonds : angle 3.94380 ( 2097) *********************** 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 258 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: B 294 MET cc_start: 0.5755 (tpt) cc_final: 0.5416 (tpt) REVERT: C 250 PHE cc_start: 0.8173 (t80) cc_final: 0.7962 (t80) REVERT: D 176 MET cc_start: 0.8716 (tmm) cc_final: 0.8473 (ppp) REVERT: D 294 MET cc_start: 0.5718 (tpt) cc_final: 0.5110 (tpp) REVERT: E 176 MET cc_start: 0.8546 (tmm) cc_final: 0.8167 (ttt) REVERT: L 80 ASP cc_start: 0.7847 (t0) cc_final: 0.7626 (t0) REVERT: L 99 GLN cc_start: 0.7665 (mm-40) cc_final: 0.6725 (mt0) REVERT: N 99 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7191 (mt0) REVERT: O 54 THR cc_start: 0.8683 (p) cc_final: 0.8369 (t) REVERT: P 62 GLN cc_start: 0.7924 (mp10) cc_final: 0.7346 (pt0) outliers start: 35 outliers final: 32 residues processed: 240 average time/residue: 0.0628 time to fit residues: 23.9471 Evaluate side-chains 248 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 267 CYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 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 118 optimal weight: 1.9990 chunk 105 optimal weight: 0.0370 chunk 62 optimal weight: 0.0570 chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.179398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.145340 restraints weight = 14137.265| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.34 r_work: 0.3710 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10782 Z= 0.128 Angle : 0.599 11.095 14756 Z= 0.297 Chirality : 0.039 0.225 1797 Planarity : 0.004 0.046 1802 Dihedral : 3.603 17.450 1489 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.26 % Allowed : 23.42 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.23), residues: 1390 helix: 3.03 (0.18), residues: 666 sheet: -0.29 (0.31), residues: 294 loop : -1.42 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 123 TYR 0.012 0.001 TYR O 126 PHE 0.025 0.001 PHE O 52 TRP 0.007 0.001 TRP F 280 HIS 0.005 0.001 HIS H 58 Details of bonding type rmsd covalent geometry : bond 0.00287 (10777) covalent geometry : angle 0.59906 (14746) SS BOND : bond 0.00200 ( 5) SS BOND : angle 0.29120 ( 10) hydrogen bonds : bond 0.03817 ( 717) hydrogen bonds : angle 3.93939 ( 2097) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2780 Ramachandran restraints generated. 1390 Oldfield, 0 Emsley, 1390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.384 Fit side-chains REVERT: B 294 MET cc_start: 0.5736 (tpt) cc_final: 0.5406 (tpt) REVERT: C 163 LYS cc_start: 0.8652 (tptt) cc_final: 0.8430 (tptp) REVERT: C 250 PHE cc_start: 0.8173 (t80) cc_final: 0.7956 (t80) REVERT: D 176 MET cc_start: 0.8731 (tmm) cc_final: 0.8504 (ppp) REVERT: D 294 MET cc_start: 0.5623 (tpt) cc_final: 0.5007 (tpp) REVERT: E 176 MET cc_start: 0.8565 (tmm) cc_final: 0.8294 (ttt) REVERT: L 62 GLN cc_start: 0.7901 (mp10) cc_final: 0.7207 (pt0) REVERT: L 80 ASP cc_start: 0.7844 (t0) cc_final: 0.7638 (t0) REVERT: L 99 GLN cc_start: 0.7689 (mm-40) cc_final: 0.6809 (mt0) REVERT: N 62 GLN cc_start: 0.7918 (mp10) cc_final: 0.7246 (pt0) REVERT: N 99 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7262 (mt0) REVERT: O 54 THR cc_start: 0.8657 (p) cc_final: 0.8291 (t) REVERT: P 62 GLN cc_start: 0.7909 (mp10) cc_final: 0.7378 (pt0) REVERT: P 99 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7367 (mt0) outliers start: 34 outliers final: 30 residues processed: 239 average time/residue: 0.0727 time to fit residues: 27.2178 Evaluate side-chains 249 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 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 H residue 28 VAL Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 45 CYS Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain M residue 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 74 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.0050 chunk 17 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 42 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.181241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.145177 restraints weight = 14484.528| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.31 r_work: 0.3744 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3756 r_free = 0.3756 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10782 Z= 0.119 Angle : 0.592 11.440 14756 Z= 0.292 Chirality : 0.039 0.243 1797 Planarity : 0.004 0.065 1802 Dihedral : 3.557 17.011 1489 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.07 % Allowed : 23.42 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.23), residues: 1390 helix: 3.11 (0.18), residues: 666 sheet: -0.38 (0.31), residues: 306 loop : -1.37 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 123 TYR 0.020 0.001 TYR O 55 PHE 0.021 0.001 PHE O 52 TRP 0.007 0.001 TRP F 280 HIS 0.005 0.001 HIS M 58 Details of bonding type rmsd covalent geometry : bond 0.00261 (10777) covalent geometry : angle 0.59227 (14746) SS BOND : bond 0.00175 ( 5) SS BOND : angle 0.28938 ( 10) hydrogen bonds : bond 0.03687 ( 717) hydrogen bonds : angle 3.87833 ( 2097) =============================================================================== Job complete usr+sys time: 2408.55 seconds wall clock time: 42 minutes 2.10 seconds (2522.10 seconds total)