Starting phenix.real_space_refine on Sat May 17 20:14:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyd_18751/05_2025/8qyd_18751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyd_18751/05_2025/8qyd_18751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyd_18751/05_2025/8qyd_18751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyd_18751/05_2025/8qyd_18751.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyd_18751/05_2025/8qyd_18751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyd_18751/05_2025/8qyd_18751.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= -0.000 sd= 0.068 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 49 5.16 5 C 10318 2.51 5 N 2515 2.21 5 O 3248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16150 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2231 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 271} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 271} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2260 Chain: "B" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 271} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 270} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 271} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 271} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain: "G" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {' CA': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 203 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 13.54, per 1000 atoms: 0.84 Number of scatterers: 16150 At special positions: 0 Unit cell: (83.2, 80.704, 248.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 49 16.00 P 15 15.00 O 3248 8.00 N 2515 7.00 C 10318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 86 " distance=2.03 Simple disulfide: pdb=" SG CYS F 165 " - pdb=" SG CYS F 240 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 86 " distance=2.03 Simple disulfide: pdb=" SG CYS G 165 " - pdb=" SG CYS G 240 " 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: 4.65 Conformation dependent library (CDL) restraints added in 2.6 seconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 7 sheets defined 78.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 17 through 38 Processing helix chain 'A' and resid 38 through 58 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 134 through 158 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 165 through 218 Processing helix chain 'A' and resid 223 through 280 removed outlier: 3.667A pdb=" N GLU A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 13 through 14 No H-bonds generated for 'chain 'B' and resid 13 through 14' Processing helix chain 'B' and resid 15 through 16 No H-bonds generated for 'chain 'B' and resid 15 through 16' Processing helix chain 'B' and resid 17 through 38 Processing helix chain 'B' and resid 38 through 57 Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 134 through 158 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 165 through 220 removed outlier: 3.761A pdb=" N LEU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 280 removed outlier: 3.781A pdb=" N THR B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 17 through 38 Processing helix chain 'C' and resid 38 through 59 Processing helix chain 'C' and resid 63 through 75 Processing helix chain 'C' and resid 77 through 90 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 162 through 218 Processing helix chain 'C' and resid 223 through 280 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 17 through 38 removed outlier: 3.511A pdb=" N VAL D 21 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 58 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.277A pdb=" N ARG D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 134 through 158 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 165 through 218 Processing helix chain 'D' and resid 223 through 280 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 13 through 14 No H-bonds generated for 'chain 'E' and resid 13 through 14' Processing helix chain 'E' and resid 15 through 16 No H-bonds generated for 'chain 'E' and resid 15 through 16' Processing helix chain 'E' and resid 17 through 38 Processing helix chain 'E' and resid 38 through 58 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 77 through 91 Processing helix chain 'E' and resid 112 through 116 Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 134 through 157 removed outlier: 3.503A pdb=" N HIS E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 218 Processing helix chain 'E' and resid 223 through 280 removed outlier: 3.706A pdb=" N GLU E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 79 Processing helix chain 'F' and resid 107 through 127 removed outlier: 3.717A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 148 through 169 Processing helix chain 'F' and resid 172 through 178 removed outlier: 3.885A pdb=" N LYS F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 189 Processing helix chain 'F' and resid 203 through 208 removed outlier: 3.505A pdb=" N ARG F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 47 removed outlier: 3.920A pdb=" N ILE G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 79 Processing helix chain 'G' and resid 107 through 127 removed outlier: 3.635A pdb=" N GLN G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 127 through 133 Processing helix chain 'G' and resid 148 through 168 removed outlier: 3.528A pdb=" N ASN G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 177 removed outlier: 3.587A pdb=" N LYS G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN G 177 " --> pdb=" O PRO G 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 177' Processing helix chain 'G' and resid 179 through 189 Processing helix chain 'G' and resid 224 through 228 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 98 removed outlier: 3.630A pdb=" N ARG A 106 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 96 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE A 104 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU A 98 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 98 removed outlier: 3.655A pdb=" N ARG B 106 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B 96 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE B 104 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU B 98 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 97 removed outlier: 3.647A pdb=" N ARG C 106 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU C 96 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE C 104 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 98 removed outlier: 3.554A pdb=" N ARG D 106 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU D 96 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE D 104 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU D 98 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 92 through 98 removed outlier: 3.771A pdb=" N ARG E 106 " --> pdb=" O GLN E 94 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU E 96 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE E 104 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU E 98 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 82 through 85 removed outlier: 4.922A pdb=" N PHE F 93 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL F 210 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLU F 211 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE F 139 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG F 213 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE F 137 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN F 215 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 11.822A pdb=" N LYS F 135 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ALA F 192 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ILE F 137 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N GLY F 194 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE F 139 " --> pdb=" O GLY F 194 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER F 196 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLY F 141 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 83 through 85 removed outlier: 3.784A pdb=" N GLU G 211 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN G 215 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN G 136 " --> pdb=" O GLN G 215 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N LEU G 191 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE G 137 " --> pdb=" O LEU G 191 " (cutoff:3.500A) 1197 hydrogen bonds defined for protein. 3540 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: 5.25 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2509 1.31 - 1.44: 4155 1.44 - 1.56: 9233 1.56 - 1.69: 136 1.69 - 1.82: 95 Bond restraints: 16128 Sorted by residual: bond pdb=" C38 PEE B 803 " pdb=" C39 PEE B 803 " ideal model delta sigma weight residual 1.523 1.353 0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" C38 PEE C 802 " pdb=" C39 PEE C 802 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.18e+01 bond pdb=" C38 PEE D 802 " pdb=" C39 PEE D 802 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.17e+01 bond pdb=" C38 PEE E 802 " pdb=" C39 PEE E 802 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C38 PEE B 801 " pdb=" C39 PEE B 801 " ideal model delta sigma weight residual 1.523 1.355 0.168 2.00e-02 2.50e+03 7.09e+01 ... (remaining 16123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.42: 21596 10.42 - 20.84: 20 20.84 - 31.25: 1 31.25 - 41.67: 0 41.67 - 52.09: 10 Bond angle restraints: 21627 Sorted by residual: angle pdb=" C38 PEE B 801 " pdb=" C39 PEE B 801 " pdb=" C40 PEE B 801 " ideal model delta sigma weight residual 112.47 164.56 -52.09 3.00e+00 1.11e-01 3.01e+02 angle pdb=" C38 PEE D 802 " pdb=" C39 PEE D 802 " pdb=" C40 PEE D 802 " ideal model delta sigma weight residual 112.47 164.55 -52.08 3.00e+00 1.11e-01 3.01e+02 angle pdb=" C38 PEE E 802 " pdb=" C39 PEE E 802 " pdb=" C40 PEE E 802 " ideal model delta sigma weight residual 112.47 164.07 -51.60 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C38 PEE C 802 " pdb=" C39 PEE C 802 " pdb=" C40 PEE C 802 " ideal model delta sigma weight residual 112.47 163.89 -51.42 3.00e+00 1.11e-01 2.94e+02 angle pdb=" C38 PEE B 803 " pdb=" C39 PEE B 803 " pdb=" C40 PEE B 803 " ideal model delta sigma weight residual 112.47 163.82 -51.35 3.00e+00 1.11e-01 2.93e+02 ... (remaining 21622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 9576 33.69 - 67.38: 333 67.38 - 101.07: 36 101.07 - 134.77: 19 134.77 - 168.46: 9 Dihedral angle restraints: 9973 sinusoidal: 4401 harmonic: 5572 Sorted by residual: dihedral pdb=" CD ARG A 77 " pdb=" NE ARG A 77 " pdb=" CZ ARG A 77 " pdb=" NH1 ARG A 77 " ideal model delta sinusoidal sigma weight residual 0.00 -83.11 83.11 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CD ARG B 77 " pdb=" NE ARG B 77 " pdb=" CZ ARG B 77 " pdb=" NH1 ARG B 77 " ideal model delta sinusoidal sigma weight residual 0.00 -76.34 76.34 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" C ARG B 77 " pdb=" N ARG B 77 " pdb=" CA ARG B 77 " pdb=" CB ARG B 77 " ideal model delta harmonic sigma weight residual -122.60 -140.07 17.47 0 2.50e+00 1.60e-01 4.88e+01 ... (remaining 9970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2362 0.115 - 0.230: 22 0.230 - 0.345: 0 0.345 - 0.460: 0 0.460 - 0.575: 6 Chirality restraints: 2390 Sorted by residual: chirality pdb=" C2 PEE B 803 " pdb=" C1 PEE B 803 " pdb=" C3 PEE B 803 " pdb=" O2 PEE B 803 " both_signs ideal model delta sigma weight residual False -2.33 -2.90 0.58 2.00e-01 2.50e+01 8.27e+00 chirality pdb=" C2 PEE E 802 " pdb=" C1 PEE E 802 " pdb=" C3 PEE E 802 " pdb=" O2 PEE E 802 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C2 PEE C 802 " pdb=" C1 PEE C 802 " pdb=" C3 PEE C 802 " pdb=" O2 PEE C 802 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.24e+00 ... (remaining 2387 not shown) Planarity restraints: 2660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 77 " -1.084 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARG A 77 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 77 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 77 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 77 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 77 " 1.073 9.50e-02 1.11e+02 4.81e-01 1.39e+02 pdb=" NE ARG B 77 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 77 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 77 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 77 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 77 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ARG A 77 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG A 77 " -0.024 2.00e-02 2.50e+03 pdb=" N SER A 78 " -0.023 2.00e-02 2.50e+03 ... (remaining 2657 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 450 2.70 - 3.25: 15856 3.25 - 3.80: 27534 3.80 - 4.35: 34858 4.35 - 4.90: 59157 Nonbonded interactions: 137855 Sorted by model distance: nonbonded pdb=" OE1 GLU F 95 " pdb=" NE ARG F 98 " model vdw 2.152 3.120 nonbonded pdb=" OE1 GLU A 210 " pdb=" O HOH A 901 " model vdw 2.161 3.040 nonbonded pdb=" N LEU A 80 " pdb=" O HOH A 902 " model vdw 2.167 3.120 nonbonded pdb="CA CA E 803 " pdb=" O HOH A 906 " model vdw 2.167 2.510 nonbonded pdb=" OH TYR E 208 " pdb=" OA4 CDL E 801 " model vdw 2.172 3.040 ... (remaining 137850 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 1 through 174 or resid 176 through 280)) selection = (chain 'B' and (resid 1 through 174 or resid 176 through 280)) selection = (chain 'C' and (resid 1 through 174 or resid 176 through 280)) selection = (chain 'D' and (resid 1 through 174 or resid 176 through 280)) selection = (chain 'E' and (resid 1 through 174 or resid 176 through 280)) } ncs_group { reference = chain 'F' selection = chain 'G' } 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=0.00 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: 11.900 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 41.790 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 : 0.008 0.170 16132 Z= 0.415 Angle : 1.365 52.091 21635 Z= 0.531 Chirality : 0.048 0.575 2390 Planarity : 0.014 0.486 2660 Dihedral : 18.408 168.458 6337 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.52 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.19), residues: 1880 helix: 3.23 (0.13), residues: 1280 sheet: -0.45 (0.78), residues: 50 loop : -0.31 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 PHE 0.016 0.002 PHE G 217 TYR 0.017 0.001 TYR D 208 ARG 0.008 0.001 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.11035 ( 1197) hydrogen bonds : angle 4.60306 ( 3540) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.59503 ( 8) covalent geometry : bond 0.00833 (16128) covalent geometry : angle 1.36487 (21627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7499 (mp0) cc_final: 0.7284 (mp0) REVERT: B 96 GLU cc_start: 0.6549 (pt0) cc_final: 0.6209 (pt0) REVERT: D 44 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7858 (mtm110) REVERT: D 69 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7252 (mm-30) REVERT: D 234 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7639 (ttmt) REVERT: E 81 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8156 (ttpm) REVERT: E 103 LYS cc_start: 0.8157 (ptmm) cc_final: 0.7953 (ptmt) REVERT: E 175 ARG cc_start: 0.8035 (ttp-110) cc_final: 0.7794 (ttp-110) REVERT: F 58 LYS cc_start: 0.7113 (ttpt) cc_final: 0.6859 (tttp) REVERT: F 217 PHE cc_start: 0.5851 (m-80) cc_final: 0.5344 (m-10) REVERT: G 76 ARG cc_start: 0.3182 (mmp80) cc_final: 0.2835 (mtm180) REVERT: G 213 ARG cc_start: 0.5528 (tmt170) cc_final: 0.5145 (tpt90) outliers start: 2 outliers final: 0 residues processed: 216 average time/residue: 1.6035 time to fit residues: 376.5257 Evaluate side-chains 160 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 234 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 3.9990 chunk 142 optimal weight: 0.0980 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN D 134 HIS E 5 ASN F 158 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN G 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.188408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113752 restraints weight = 19506.910| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.72 r_work: 0.3124 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16132 Z= 0.139 Angle : 0.508 7.638 21635 Z= 0.261 Chirality : 0.038 0.155 2390 Planarity : 0.004 0.059 2660 Dihedral : 18.323 178.119 2751 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.91 % Allowed : 6.60 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.19), residues: 1880 helix: 3.50 (0.13), residues: 1283 sheet: -0.42 (0.83), residues: 48 loop : -0.36 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 196 HIS 0.005 0.001 HIS A 92 PHE 0.011 0.001 PHE E 75 TYR 0.018 0.001 TYR E 208 ARG 0.007 0.000 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.04855 ( 1197) hydrogen bonds : angle 3.80985 ( 3540) SS BOND : bond 0.00150 ( 4) SS BOND : angle 0.63344 ( 8) covalent geometry : bond 0.00310 (16128) covalent geometry : angle 0.50757 (21627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7483 (mtpp) REVERT: C 69 GLU cc_start: 0.8230 (tp30) cc_final: 0.7899 (tp30) REVERT: D 60 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7259 (mt-10) REVERT: D 69 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7372 (mm-30) REVERT: E 81 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8135 (ttpt) REVERT: E 103 LYS cc_start: 0.8123 (ptmm) cc_final: 0.7858 (ptmt) REVERT: E 175 ARG cc_start: 0.7874 (ttp-110) cc_final: 0.7637 (ttp-110) REVERT: F 12 ARG cc_start: 0.5028 (tmt170) cc_final: 0.4466 (tmm160) REVERT: F 95 GLU cc_start: 0.6122 (tp30) cc_final: 0.5436 (pm20) REVERT: F 217 PHE cc_start: 0.5935 (m-80) cc_final: 0.5433 (m-10) outliers start: 15 outliers final: 7 residues processed: 181 average time/residue: 1.5016 time to fit residues: 297.9764 Evaluate side-chains 164 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 186 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 ASN E 5 ASN ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108581 restraints weight = 25263.330| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.00 r_work: 0.2987 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16132 Z= 0.177 Angle : 0.510 7.180 21635 Z= 0.266 Chirality : 0.039 0.158 2390 Planarity : 0.004 0.061 2660 Dihedral : 17.734 178.456 2747 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.33 % Allowed : 8.24 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.19), residues: 1880 helix: 3.43 (0.13), residues: 1284 sheet: -0.42 (0.79), residues: 55 loop : -0.38 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 PHE 0.014 0.002 PHE E 181 TYR 0.024 0.001 TYR E 208 ARG 0.008 0.001 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.05116 ( 1197) hydrogen bonds : angle 3.76691 ( 3540) SS BOND : bond 0.00105 ( 4) SS BOND : angle 0.43431 ( 8) covalent geometry : bond 0.00423 (16128) covalent geometry : angle 0.51006 (21627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.759 Fit side-chains REVERT: A 103 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7540 (mtpp) REVERT: C 7 ILE cc_start: 0.8207 (mp) cc_final: 0.7998 (mp) REVERT: D 60 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7328 (mt-10) REVERT: D 69 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7355 (mm-30) REVERT: D 79 GLU cc_start: 0.8189 (pm20) cc_final: 0.7974 (pm20) REVERT: E 121 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8155 (mp10) REVERT: E 257 MET cc_start: 0.7426 (mtp) cc_final: 0.7217 (mtp) REVERT: F 12 ARG cc_start: 0.5149 (tmt170) cc_final: 0.4633 (tmm160) REVERT: G 111 GLN cc_start: 0.2087 (OUTLIER) cc_final: 0.1684 (pt0) outliers start: 22 outliers final: 10 residues processed: 178 average time/residue: 1.5776 time to fit residues: 306.9417 Evaluate side-chains 161 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 111 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 157 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 111 GLN ** 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 = 0.4109 r_free = 0.4109 target = 0.186039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109582 restraints weight = 24523.049| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.98 r_work: 0.3007 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16132 Z= 0.150 Angle : 0.495 12.893 21635 Z= 0.252 Chirality : 0.038 0.163 2390 Planarity : 0.004 0.060 2660 Dihedral : 17.461 178.569 2747 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.39 % Allowed : 9.93 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.19), residues: 1880 helix: 3.50 (0.13), residues: 1284 sheet: -0.50 (0.85), residues: 46 loop : -0.43 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.025 0.001 PHE F 217 TYR 0.021 0.001 TYR E 208 ARG 0.007 0.000 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 1197) hydrogen bonds : angle 3.68290 ( 3540) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.35071 ( 8) covalent geometry : bond 0.00353 (16128) covalent geometry : angle 0.49513 (21627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.772 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7563 (mtpp) REVERT: C 7 ILE cc_start: 0.8249 (mp) cc_final: 0.8021 (mp) REVERT: C 69 GLU cc_start: 0.8269 (tp30) cc_final: 0.7942 (tp30) REVERT: C 248 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6473 (mt-10) REVERT: D 60 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7291 (mt-10) REVERT: D 69 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7362 (mm-30) REVERT: D 79 GLU cc_start: 0.8214 (pm20) cc_final: 0.7999 (pm20) REVERT: E 121 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: F 12 ARG cc_start: 0.5098 (tmt170) cc_final: 0.4878 (tmm160) REVERT: F 217 PHE cc_start: 0.5703 (m-80) cc_final: 0.5213 (m-10) REVERT: G 12 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.5726 (tpp-160) REVERT: G 111 GLN cc_start: 0.2577 (OUTLIER) cc_final: 0.2295 (tt0) outliers start: 23 outliers final: 10 residues processed: 177 average time/residue: 1.4540 time to fit residues: 283.7605 Evaluate side-chains 171 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 111 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 80 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 121 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN D 120 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.186693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112599 restraints weight = 20252.336| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.72 r_work: 0.3057 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16132 Z= 0.143 Angle : 0.479 10.984 21635 Z= 0.246 Chirality : 0.037 0.169 2390 Planarity : 0.004 0.059 2660 Dihedral : 17.095 178.835 2747 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.64 % Allowed : 10.72 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.19), residues: 1880 helix: 3.58 (0.13), residues: 1305 sheet: -0.49 (0.84), residues: 46 loop : -0.39 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.020 0.001 PHE F 217 TYR 0.020 0.001 TYR E 208 ARG 0.009 0.000 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.04693 ( 1197) hydrogen bonds : angle 3.62532 ( 3540) SS BOND : bond 0.00115 ( 4) SS BOND : angle 0.41539 ( 8) covalent geometry : bond 0.00333 (16128) covalent geometry : angle 0.47934 (21627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 1.893 Fit side-chains REVERT: A 103 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7571 (mtpp) REVERT: A 120 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: C 7 ILE cc_start: 0.8222 (mp) cc_final: 0.7971 (mp) REVERT: C 69 GLU cc_start: 0.8264 (tp30) cc_final: 0.7908 (tp30) REVERT: C 248 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6496 (mt-10) REVERT: D 69 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7372 (mm-30) REVERT: E 121 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: E 257 MET cc_start: 0.7207 (mtp) cc_final: 0.6827 (mtm) REVERT: F 12 ARG cc_start: 0.5050 (tmt170) cc_final: 0.4846 (tmm160) REVERT: F 217 PHE cc_start: 0.5959 (m-80) cc_final: 0.5408 (m-10) REVERT: G 12 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.5752 (tpp-160) outliers start: 27 outliers final: 12 residues processed: 182 average time/residue: 1.5004 time to fit residues: 299.5237 Evaluate side-chains 171 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.186838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112089 restraints weight = 22699.115| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.79 r_work: 0.3051 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16132 Z= 0.139 Angle : 0.480 9.778 21635 Z= 0.246 Chirality : 0.037 0.235 2390 Planarity : 0.004 0.060 2660 Dihedral : 16.811 179.516 2747 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.21 % Allowed : 11.57 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.19), residues: 1880 helix: 3.56 (0.13), residues: 1287 sheet: -0.31 (0.99), residues: 36 loop : -0.30 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.018 0.001 PHE F 217 TYR 0.020 0.001 TYR E 208 ARG 0.008 0.000 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 1197) hydrogen bonds : angle 3.61302 ( 3540) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.36829 ( 8) covalent geometry : bond 0.00323 (16128) covalent geometry : angle 0.48030 (21627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.639 Fit side-chains REVERT: A 103 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7578 (mtpp) REVERT: C 7 ILE cc_start: 0.8241 (mp) cc_final: 0.7984 (mp) REVERT: C 248 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6555 (mt-10) REVERT: D 69 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7413 (mm-30) REVERT: D 121 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8650 (tt0) REVERT: E 121 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: F 217 PHE cc_start: 0.6065 (m-80) cc_final: 0.5490 (m-10) REVERT: G 12 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5735 (tpp-160) REVERT: G 167 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5819 (mm) outliers start: 20 outliers final: 11 residues processed: 176 average time/residue: 1.4733 time to fit residues: 284.8293 Evaluate side-chains 170 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 78 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 122 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.186899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112865 restraints weight = 24701.730| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.21 r_work: 0.3039 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16132 Z= 0.135 Angle : 0.480 8.609 21635 Z= 0.247 Chirality : 0.037 0.179 2390 Planarity : 0.004 0.063 2660 Dihedral : 16.459 179.393 2747 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.15 % Allowed : 11.93 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.19), residues: 1880 helix: 3.66 (0.13), residues: 1303 sheet: -0.25 (0.99), residues: 36 loop : -0.34 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.017 0.001 PHE F 217 TYR 0.018 0.001 TYR E 208 ARG 0.009 0.000 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 1197) hydrogen bonds : angle 3.58157 ( 3540) SS BOND : bond 0.00131 ( 4) SS BOND : angle 0.38261 ( 8) covalent geometry : bond 0.00314 (16128) covalent geometry : angle 0.47981 (21627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7576 (mtpp) REVERT: C 7 ILE cc_start: 0.8209 (mp) cc_final: 0.7959 (mp) REVERT: C 69 GLU cc_start: 0.8242 (tp30) cc_final: 0.7929 (tp30) REVERT: C 248 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6520 (mt-10) REVERT: D 69 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7453 (mm-30) REVERT: D 121 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8674 (tt0) REVERT: E 79 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6495 (pt0) REVERT: G 12 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.5737 (tpp-160) REVERT: G 190 PHE cc_start: 0.6387 (m-80) cc_final: 0.5327 (m-80) outliers start: 19 outliers final: 11 residues processed: 173 average time/residue: 1.3795 time to fit residues: 265.3572 Evaluate side-chains 169 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 83 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 141 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.186265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111990 restraints weight = 24431.222| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.22 r_work: 0.2997 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16132 Z= 0.153 Angle : 0.494 8.673 21635 Z= 0.255 Chirality : 0.038 0.184 2390 Planarity : 0.004 0.064 2660 Dihedral : 16.376 179.518 2747 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.33 % Allowed : 12.66 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.19), residues: 1880 helix: 3.56 (0.13), residues: 1287 sheet: -0.27 (0.99), residues: 36 loop : -0.28 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 PHE 0.016 0.001 PHE G 197 TYR 0.019 0.001 TYR E 208 ARG 0.010 0.000 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 1197) hydrogen bonds : angle 3.61594 ( 3540) SS BOND : bond 0.00117 ( 4) SS BOND : angle 0.31142 ( 8) covalent geometry : bond 0.00361 (16128) covalent geometry : angle 0.49370 (21627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7566 (mtpp) REVERT: C 7 ILE cc_start: 0.8194 (mp) cc_final: 0.7931 (mp) REVERT: C 69 GLU cc_start: 0.8303 (tp30) cc_final: 0.7969 (tp30) REVERT: C 248 GLU cc_start: 0.6782 (mt-10) cc_final: 0.6518 (mt-10) REVERT: D 121 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: E 121 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: F 217 PHE cc_start: 0.5631 (m-10) cc_final: 0.5265 (m-10) REVERT: G 12 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.5759 (tpp-160) REVERT: G 190 PHE cc_start: 0.6368 (m-80) cc_final: 0.5281 (m-80) outliers start: 22 outliers final: 11 residues processed: 174 average time/residue: 1.4282 time to fit residues: 273.9034 Evaluate side-chains 172 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 117 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 85 optimal weight: 0.0270 chunk 127 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.187426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112414 restraints weight = 23493.135| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.83 r_work: 0.3057 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16132 Z= 0.130 Angle : 0.480 7.494 21635 Z= 0.248 Chirality : 0.037 0.189 2390 Planarity : 0.004 0.064 2660 Dihedral : 16.092 179.101 2747 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.03 % Allowed : 13.45 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.19), residues: 1880 helix: 3.74 (0.13), residues: 1296 sheet: -0.33 (0.86), residues: 48 loop : -0.35 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 196 HIS 0.003 0.000 HIS D 82 PHE 0.012 0.001 PHE A 181 TYR 0.017 0.001 TYR E 208 ARG 0.011 0.000 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 1197) hydrogen bonds : angle 3.56158 ( 3540) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.28860 ( 8) covalent geometry : bond 0.00297 (16128) covalent geometry : angle 0.48007 (21627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7603 (mtpp) REVERT: B 254 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7226 (mp) REVERT: C 7 ILE cc_start: 0.8218 (mp) cc_final: 0.7956 (mp) REVERT: C 69 GLU cc_start: 0.8221 (tp30) cc_final: 0.7891 (tp30) REVERT: C 248 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6566 (mt-10) REVERT: D 69 GLU cc_start: 0.8299 (pt0) cc_final: 0.7598 (mm-30) REVERT: F 217 PHE cc_start: 0.5684 (m-10) cc_final: 0.5309 (m-10) REVERT: G 12 ARG cc_start: 0.6591 (OUTLIER) cc_final: 0.5728 (tpp-160) REVERT: G 190 PHE cc_start: 0.6365 (m-80) cc_final: 0.5255 (m-80) outliers start: 17 outliers final: 12 residues processed: 177 average time/residue: 1.2536 time to fit residues: 246.8915 Evaluate side-chains 174 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 179 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 22 optimal weight: 0.0000 chunk 173 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.183803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109629 restraints weight = 19535.246| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.67 r_work: 0.3044 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 16132 Z= 0.227 Angle : 0.564 8.503 21635 Z= 0.290 Chirality : 0.041 0.195 2390 Planarity : 0.004 0.066 2660 Dihedral : 16.702 178.179 2747 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.09 % Allowed : 13.63 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.19), residues: 1880 helix: 3.32 (0.13), residues: 1287 sheet: -0.46 (0.99), residues: 38 loop : -0.28 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 196 HIS 0.005 0.001 HIS D 82 PHE 0.017 0.002 PHE A 181 TYR 0.024 0.002 TYR E 208 ARG 0.011 0.001 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.05408 ( 1197) hydrogen bonds : angle 3.81020 ( 3540) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.34549 ( 8) covalent geometry : bond 0.00554 (16128) covalent geometry : angle 0.56441 (21627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7630 (mtpp) REVERT: B 167 SER cc_start: 0.8786 (m) cc_final: 0.8497 (p) REVERT: B 254 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7370 (mp) REVERT: C 7 ILE cc_start: 0.8308 (mp) cc_final: 0.8052 (mp) REVERT: C 248 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6659 (mt-10) REVERT: C 257 MET cc_start: 0.7257 (mtm) cc_final: 0.7042 (mtm) REVERT: D 69 GLU cc_start: 0.8294 (pt0) cc_final: 0.7636 (mm-30) REVERT: D 121 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8557 (tt0) REVERT: E 121 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: F 217 PHE cc_start: 0.5547 (m-10) cc_final: 0.5249 (m-10) REVERT: F 244 MET cc_start: 0.0927 (mmp) cc_final: -0.0654 (ptp) REVERT: G 12 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5758 (tpp-160) outliers start: 18 outliers final: 8 residues processed: 175 average time/residue: 1.3679 time to fit residues: 264.0632 Evaluate side-chains 170 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 31 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.186035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111087 restraints weight = 24215.368| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.86 r_work: 0.3021 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16132 Z= 0.144 Angle : 0.499 7.043 21635 Z= 0.258 Chirality : 0.037 0.203 2390 Planarity : 0.004 0.065 2660 Dihedral : 16.269 176.352 2747 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.91 % Allowed : 13.93 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.19), residues: 1880 helix: 3.54 (0.13), residues: 1280 sheet: -0.25 (0.87), residues: 48 loop : -0.26 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.013 0.001 PHE A 181 TYR 0.018 0.001 TYR E 208 ARG 0.011 0.000 ARG E 244 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 1197) hydrogen bonds : angle 3.64916 ( 3540) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.31166 ( 8) covalent geometry : bond 0.00338 (16128) covalent geometry : angle 0.49944 (21627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15147.72 seconds wall clock time: 261 minutes 54.63 seconds (15714.63 seconds total)