Starting phenix.real_space_refine on Sun Aug 24 01:43:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyd_18751/08_2025/8qyd_18751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyd_18751/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qyd_18751/08_2025/8qyd_18751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyd_18751/08_2025/8qyd_18751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qyd_18751/08_2025/8qyd_18751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyd_18751/08_2025/8qyd_18751.map" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 1, 'TYR:plan': 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: {'ASN:plan1': 1, 'TYR:plan': 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: {'ASN:plan1': 1, 'TYR:plan': 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: {'ASN:plan1': 1, 'TYR:plan': 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: {'ASN:plan1': 1, 'TYR:plan': 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: {'ASN:plan1': 1, 'TYR:plan': 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: 3.59, per 1000 atoms: 0.22 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: 1.40 Conformation dependent library (CDL) restraints added in 684.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 2.08 Time building geometry restraints manager: 1.87 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: 8.020 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.940 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.130 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG B 54 TYR 0.017 0.001 TYR D 208 PHE 0.016 0.002 PHE G 217 TRP 0.028 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00833 (16128) covalent geometry : angle 1.36487 (21627) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.59503 ( 8) hydrogen bonds : bond 0.11035 ( 1197) hydrogen bonds : angle 4.60306 ( 3540) *********************** 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 : 0.656 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: 0.7228 (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: 0.7331 time to fit residues: 171.3945 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 : 0.590 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.187818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111416 restraints weight = 23122.848| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.95 r_work: 0.3064 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 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 = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16132 Z= 0.151 Angle : 0.516 7.653 21635 Z= 0.266 Chirality : 0.038 0.155 2390 Planarity : 0.004 0.060 2660 Dihedral : 18.339 177.261 2751 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.03 % Allowed : 6.36 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.48 (0.19), residues: 1880 helix: 3.45 (0.13), residues: 1283 sheet: -0.43 (0.83), residues: 48 loop : -0.37 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 244 TYR 0.020 0.001 TYR E 208 PHE 0.012 0.001 PHE E 75 TRP 0.021 0.002 TRP A 196 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00347 (16128) covalent geometry : angle 0.51606 (21627) SS BOND : bond 0.00158 ( 4) SS BOND : angle 0.68549 ( 8) hydrogen bonds : bond 0.04966 ( 1197) hydrogen bonds : angle 3.82498 ( 3540) *********************** 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 194 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7551 (mtpp) REVERT: B 96 GLU cc_start: 0.6885 (pt0) cc_final: 0.6675 (pt0) REVERT: C 69 GLU cc_start: 0.8312 (tp30) cc_final: 0.7988 (tp30) REVERT: D 60 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7318 (mt-10) REVERT: D 69 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7452 (mm-30) REVERT: D 79 GLU cc_start: 0.8220 (pm20) cc_final: 0.7986 (pm20) REVERT: E 81 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8240 (ttpt) REVERT: E 103 LYS cc_start: 0.8191 (ptmm) cc_final: 0.7934 (ptmt) REVERT: E 175 ARG cc_start: 0.8020 (ttp-110) cc_final: 0.7790 (ttp-110) REVERT: E 238 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7395 (mt-10) REVERT: F 12 ARG cc_start: 0.5000 (tmt170) cc_final: 0.4503 (tmm160) REVERT: F 95 GLU cc_start: 0.6160 (tp30) cc_final: 0.5432 (pm20) REVERT: F 217 PHE cc_start: 0.5980 (m-80) cc_final: 0.5604 (m-10) REVERT: G 70 ARG cc_start: 0.1860 (OUTLIER) cc_final: 0.1278 (ptp-170) REVERT: G 111 GLN cc_start: 0.3454 (mm110) cc_final: 0.3145 (pt0) outliers start: 17 outliers final: 8 residues processed: 189 average time/residue: 0.5933 time to fit residues: 122.2028 Evaluate side-chains 167 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 E residue 182 LEU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 70 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 107 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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 = 0.4100 r_free = 0.4100 target = 0.185223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107496 restraints weight = 27337.326| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.09 r_work: 0.2988 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16132 Z= 0.191 Angle : 0.531 12.088 21635 Z= 0.273 Chirality : 0.040 0.160 2390 Planarity : 0.004 0.061 2660 Dihedral : 17.859 178.471 2747 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.39 % Allowed : 8.60 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.33 (0.19), residues: 1880 helix: 3.33 (0.13), residues: 1290 sheet: -0.60 (0.80), residues: 53 loop : -0.46 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 244 TYR 0.024 0.002 TYR E 208 PHE 0.014 0.002 PHE E 181 TRP 0.030 0.002 TRP A 196 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00460 (16128) covalent geometry : angle 0.53081 (21627) SS BOND : bond 0.00131 ( 4) SS BOND : angle 0.43970 ( 8) hydrogen bonds : bond 0.05263 ( 1197) hydrogen bonds : angle 3.80391 ( 3540) *********************** 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: 23 poor density : 164 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7558 (mtpp) REVERT: B 96 GLU cc_start: 0.7061 (pt0) cc_final: 0.6772 (pt0) REVERT: C 7 ILE cc_start: 0.8249 (mp) cc_final: 0.8042 (mp) REVERT: D 54 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7720 (mtp180) REVERT: D 60 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7376 (mt-10) REVERT: D 69 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7391 (mm-30) REVERT: D 79 GLU cc_start: 0.8205 (pm20) cc_final: 0.7970 (pm20) REVERT: E 121 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8210 (mp10) REVERT: E 257 MET cc_start: 0.7468 (mtp) cc_final: 0.7248 (mtp) REVERT: F 12 ARG cc_start: 0.5167 (tmt170) cc_final: 0.4670 (tmm160) REVERT: G 70 ARG cc_start: 0.1546 (OUTLIER) cc_final: 0.1233 (ptp-170) REVERT: G 111 GLN cc_start: 0.3499 (mm110) cc_final: 0.3149 (pt0) outliers start: 23 outliers final: 11 residues processed: 176 average time/residue: 0.6476 time to fit residues: 124.6008 Evaluate side-chains 162 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 12 THR Chi-restraints excluded: chain D residue 54 ARG 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 70 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 67 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.186669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111533 restraints weight = 25390.494| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.26 r_work: 0.3052 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 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 = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1607 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 12.394 21635 Z= 0.247 Chirality : 0.037 0.165 2390 Planarity : 0.004 0.059 2660 Dihedral : 17.423 178.470 2747 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.33 % Allowed : 10.18 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.53 (0.19), residues: 1880 helix: 3.49 (0.13), residues: 1288 sheet: -0.51 (0.84), residues: 46 loop : -0.39 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 244 TYR 0.020 0.001 TYR E 208 PHE 0.024 0.001 PHE F 217 TRP 0.026 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00322 (16128) covalent geometry : angle 0.48043 (21627) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.38172 ( 8) hydrogen bonds : bond 0.04724 ( 1197) hydrogen bonds : angle 3.66627 ( 3540) *********************** 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: 22 poor density : 163 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7619 (mtpp) REVERT: B 96 GLU cc_start: 0.7088 (pt0) cc_final: 0.6822 (pt0) REVERT: C 7 ILE cc_start: 0.8299 (mp) cc_final: 0.8065 (mp) REVERT: C 69 GLU cc_start: 0.8360 (tp30) cc_final: 0.8033 (tp30) REVERT: C 248 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6624 (mt-10) REVERT: D 60 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7317 (mt-10) REVERT: D 69 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7445 (mm-30) REVERT: D 79 GLU cc_start: 0.8252 (pm20) cc_final: 0.8027 (pm20) REVERT: E 121 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: F 12 ARG cc_start: 0.5147 (tmt170) cc_final: 0.4897 (tmm160) REVERT: F 217 PHE cc_start: 0.5794 (m-80) cc_final: 0.5354 (m-10) REVERT: G 12 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5746 (tpp-160) REVERT: G 111 GLN cc_start: 0.3380 (mm110) cc_final: 0.3103 (pt0) outliers start: 22 outliers final: 11 residues processed: 179 average time/residue: 0.6186 time to fit residues: 121.3385 Evaluate side-chains 173 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 178 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 181 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 269 ASN D 120 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.184078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108325 restraints weight = 24619.893| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.88 r_work: 0.2988 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 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 = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16132 Z= 0.209 Angle : 0.534 10.355 21635 Z= 0.275 Chirality : 0.040 0.172 2390 Planarity : 0.004 0.060 2660 Dihedral : 17.493 177.833 2747 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.64 % Allowed : 10.84 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.31 (0.19), residues: 1880 helix: 3.28 (0.13), residues: 1294 sheet: -0.55 (0.78), residues: 54 loop : -0.40 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 244 TYR 0.026 0.002 TYR E 208 PHE 0.020 0.002 PHE F 217 TRP 0.023 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00508 (16128) covalent geometry : angle 0.53402 (21627) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.40296 ( 8) hydrogen bonds : bond 0.05338 ( 1197) hydrogen bonds : angle 3.80120 ( 3540) *********************** 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 186 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7598 (mtpp) REVERT: B 96 GLU cc_start: 0.7189 (pt0) cc_final: 0.6803 (pt0) REVERT: B 167 SER cc_start: 0.8778 (m) cc_final: 0.8488 (p) REVERT: C 7 ILE cc_start: 0.8288 (mp) cc_final: 0.8034 (mp) REVERT: D 54 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7742 (mtp180) REVERT: D 60 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7358 (mt-10) REVERT: D 69 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7358 (mm-30) REVERT: D 121 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: E 121 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: E 257 MET cc_start: 0.7234 (mtp) cc_final: 0.6935 (mtm) REVERT: F 12 ARG cc_start: 0.5056 (tmt170) cc_final: 0.4828 (tmm160) REVERT: F 217 PHE cc_start: 0.5872 (m-80) cc_final: 0.5384 (m-10) REVERT: G 12 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5746 (tpp-160) outliers start: 27 outliers final: 12 residues processed: 177 average time/residue: 0.7078 time to fit residues: 136.4293 Evaluate side-chains 167 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 12 THR Chi-restraints excluded: chain D residue 54 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 156 ASN F 103 GLN G 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.185542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.110205 restraints weight = 24666.204| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.88 r_work: 0.3002 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 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 = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16132 Z= 0.160 Angle : 0.494 9.281 21635 Z= 0.255 Chirality : 0.038 0.193 2390 Planarity : 0.004 0.063 2660 Dihedral : 17.080 178.570 2747 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.33 % Allowed : 11.81 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.49 (0.19), residues: 1880 helix: 3.42 (0.13), residues: 1288 sheet: -0.22 (1.01), residues: 36 loop : -0.32 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 244 TYR 0.022 0.001 TYR E 208 PHE 0.018 0.002 PHE F 217 TRP 0.023 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00381 (16128) covalent geometry : angle 0.49422 (21627) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.36110 ( 8) hydrogen bonds : bond 0.04860 ( 1197) hydrogen bonds : angle 3.69328 ( 3540) *********************** 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 187 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.584 Fit side-chains REVERT: A 103 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7547 (mtpp) REVERT: B 96 GLU cc_start: 0.7175 (pt0) cc_final: 0.6806 (pt0) REVERT: C 7 ILE cc_start: 0.8237 (mp) cc_final: 0.7967 (mp) REVERT: C 69 GLU cc_start: 0.8295 (tp30) cc_final: 0.7970 (tp30) REVERT: C 248 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6571 (mt-10) REVERT: D 60 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7345 (mt-10) REVERT: D 69 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7382 (mm-30) REVERT: D 121 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: E 121 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: E 257 MET cc_start: 0.7307 (mtp) cc_final: 0.6948 (mtm) REVERT: F 12 ARG cc_start: 0.5121 (tmt170) cc_final: 0.4883 (tmm160) REVERT: F 217 PHE cc_start: 0.5943 (m-80) cc_final: 0.5427 (m-10) REVERT: G 12 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.5710 (tpp-160) REVERT: G 190 PHE cc_start: 0.6329 (m-80) cc_final: 0.5319 (m-80) outliers start: 22 outliers final: 13 residues processed: 177 average time/residue: 0.7109 time to fit residues: 137.6557 Evaluate side-chains 171 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 214 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 181 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 153 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 12 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112933 restraints weight = 18710.172| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.63 r_work: 0.3117 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1970 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 : 0.483 8.231 21635 Z= 0.251 Chirality : 0.037 0.177 2390 Planarity : 0.004 0.063 2660 Dihedral : 16.750 179.179 2747 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.39 % Allowed : 12.11 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.62 (0.19), residues: 1880 helix: 3.54 (0.13), residues: 1286 sheet: -0.20 (0.99), residues: 36 loop : -0.31 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 244 TYR 0.019 0.001 TYR E 208 PHE 0.017 0.001 PHE F 217 TRP 0.036 0.002 TRP A 196 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00323 (16128) covalent geometry : angle 0.48293 (21627) SS BOND : bond 0.00105 ( 4) SS BOND : angle 0.26644 ( 8) hydrogen bonds : bond 0.04642 ( 1197) hydrogen bonds : angle 3.63236 ( 3540) *********************** 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 189 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: B 96 GLU cc_start: 0.7154 (pt0) cc_final: 0.6900 (pt0) REVERT: C 7 ILE cc_start: 0.8288 (mp) cc_final: 0.8028 (mp) REVERT: C 69 GLU cc_start: 0.8286 (tp30) cc_final: 0.7940 (tp30) REVERT: C 248 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6616 (mt-10) REVERT: D 54 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7748 (mtp180) REVERT: D 69 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7401 (mm-30) REVERT: D 121 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: E 121 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: F 217 PHE cc_start: 0.6025 (m-80) cc_final: 0.5532 (m-10) REVERT: G 12 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.5754 (tpp-160) REVERT: G 167 LEU cc_start: 0.6913 (mm) cc_final: 0.6678 (tp) REVERT: G 190 PHE cc_start: 0.6359 (m-80) cc_final: 0.5304 (m-80) outliers start: 23 outliers final: 11 residues processed: 178 average time/residue: 0.6460 time to fit residues: 125.8143 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 : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 54 ARG 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 129 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 122 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 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 = 0.187110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111870 restraints weight = 24455.976| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.83 r_work: 0.3050 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 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 = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2040 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= 0.132 Angle : 0.479 8.795 21635 Z= 0.247 Chirality : 0.037 0.182 2390 Planarity : 0.004 0.064 2660 Dihedral : 16.414 179.573 2747 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.91 % Allowed : 13.14 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.19), residues: 1880 helix: 3.68 (0.13), residues: 1299 sheet: -0.15 (0.87), residues: 47 loop : -0.36 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 244 TYR 0.017 0.001 TYR E 208 PHE 0.016 0.001 PHE F 217 TRP 0.034 0.002 TRP A 196 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00306 (16128) covalent geometry : angle 0.47921 (21627) SS BOND : bond 0.00123 ( 4) SS BOND : angle 0.24193 ( 8) hydrogen bonds : bond 0.04526 ( 1197) hydrogen bonds : angle 3.58705 ( 3540) *********************** 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 179 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 GLU cc_start: 0.7128 (pt0) cc_final: 0.6859 (pt0) REVERT: C 7 ILE cc_start: 0.8217 (mp) cc_final: 0.7956 (mp) REVERT: C 69 GLU cc_start: 0.8279 (tp30) cc_final: 0.7947 (tp30) REVERT: C 248 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6484 (mt-10) REVERT: D 69 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7377 (mm-30) REVERT: D 121 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: F 217 PHE cc_start: 0.6029 (m-80) cc_final: 0.5517 (m-10) REVERT: G 12 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.5700 (tpp-160) REVERT: G 190 PHE cc_start: 0.6321 (m-80) cc_final: 0.5260 (m-80) outliers start: 15 outliers final: 11 residues processed: 174 average time/residue: 0.6173 time to fit residues: 118.2942 Evaluate side-chains 167 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 101 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 164 optimal weight: 0.0270 chunk 44 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.186110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113202 restraints weight = 17766.468| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.60 r_work: 0.3095 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2092 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= 0.141 Angle : 0.485 7.150 21635 Z= 0.251 Chirality : 0.037 0.189 2390 Planarity : 0.004 0.065 2660 Dihedral : 16.279 179.448 2747 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.39 % Allowed : 13.26 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.72 (0.19), residues: 1880 helix: 3.64 (0.13), residues: 1280 sheet: -0.23 (0.87), residues: 48 loop : -0.29 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 244 TYR 0.018 0.001 TYR E 208 PHE 0.016 0.001 PHE F 217 TRP 0.038 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00330 (16128) covalent geometry : angle 0.48465 (21627) SS BOND : bond 0.00121 ( 4) SS BOND : angle 0.24614 ( 8) hydrogen bonds : bond 0.04630 ( 1197) hydrogen bonds : angle 3.61486 ( 3540) *********************** 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 184 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 GLU cc_start: 0.7120 (pt0) cc_final: 0.6854 (pt0) REVERT: C 7 ILE cc_start: 0.8229 (mp) cc_final: 0.7969 (mp) REVERT: C 69 GLU cc_start: 0.8168 (tp30) cc_final: 0.7960 (tp30) REVERT: C 248 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6536 (mt-10) REVERT: D 54 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7668 (mtp180) REVERT: D 69 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7278 (mm-30) REVERT: D 121 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8609 (tt0) REVERT: E 121 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: F 217 PHE cc_start: 0.6004 (m-80) cc_final: 0.5481 (m-10) REVERT: G 12 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.5706 (tpp-160) REVERT: G 167 LEU cc_start: 0.6868 (mm) cc_final: 0.6623 (tp) REVERT: G 190 PHE cc_start: 0.6430 (m-80) cc_final: 0.5297 (m-80) REVERT: G 197 PHE cc_start: 0.4440 (m-80) cc_final: 0.3015 (t80) outliers start: 23 outliers final: 12 residues processed: 173 average time/residue: 0.6446 time to fit residues: 122.3993 Evaluate side-chains 173 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 251 VAL Chi-restraints excluded: chain D residue 54 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 123 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.185685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110643 restraints weight = 23119.087| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.78 r_work: 0.3077 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 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 = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16132 Z= 0.163 Angle : 0.508 8.419 21635 Z= 0.262 Chirality : 0.038 0.191 2390 Planarity : 0.004 0.065 2660 Dihedral : 16.287 179.260 2747 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.21 % Allowed : 13.63 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.63 (0.19), residues: 1880 helix: 3.55 (0.13), residues: 1280 sheet: -0.23 (0.88), residues: 48 loop : -0.28 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 244 TYR 0.020 0.001 TYR E 208 PHE 0.016 0.002 PHE F 217 TRP 0.049 0.002 TRP A 196 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00391 (16128) covalent geometry : angle 0.50791 (21627) SS BOND : bond 0.00089 ( 4) SS BOND : angle 0.25046 ( 8) hydrogen bonds : bond 0.04840 ( 1197) hydrogen bonds : angle 3.67448 ( 3540) ********************** 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 180 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 GLU cc_start: 0.7215 (pt0) cc_final: 0.6874 (pt0) REVERT: B 254 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7384 (mp) REVERT: C 7 ILE cc_start: 0.8301 (mp) cc_final: 0.8045 (mp) REVERT: C 41 ARG cc_start: 0.8501 (mtt180) cc_final: 0.8213 (mtt-85) REVERT: C 69 GLU cc_start: 0.8284 (tp30) cc_final: 0.8083 (tp30) REVERT: C 248 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6697 (mt-10) REVERT: C 257 MET cc_start: 0.7296 (mtm) cc_final: 0.6982 (mtm) REVERT: D 69 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7428 (mm-30) REVERT: D 121 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8672 (tt0) REVERT: E 79 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6548 (pt0) REVERT: E 121 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8101 (mp10) REVERT: F 217 PHE cc_start: 0.6024 (m-80) cc_final: 0.5511 (m-10) REVERT: F 244 MET cc_start: 0.0952 (mmp) cc_final: -0.0673 (ptp) REVERT: G 12 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.5731 (tpp-160) REVERT: G 190 PHE cc_start: 0.6499 (m-80) cc_final: 0.5314 (m-80) REVERT: G 197 PHE cc_start: 0.4452 (m-80) cc_final: 0.3876 (m-10) outliers start: 20 outliers final: 11 residues processed: 171 average time/residue: 0.7079 time to fit residues: 132.5868 Evaluate side-chains 176 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 E residue 182 LEU 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 61 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 112 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 22 optimal weight: 0.0000 chunk 181 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.186773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112926 restraints weight = 24462.058| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.23 r_work: 0.3043 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 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 = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2182 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= 0.126 Angle : 0.482 7.181 21635 Z= 0.248 Chirality : 0.037 0.193 2390 Planarity : 0.004 0.065 2660 Dihedral : 15.945 177.707 2747 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.97 % Allowed : 13.81 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.88 (0.19), residues: 1880 helix: 3.73 (0.13), residues: 1298 sheet: -0.16 (0.88), residues: 48 loop : -0.30 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 244 TYR 0.017 0.001 TYR E 208 PHE 0.015 0.001 PHE F 217 TRP 0.060 0.002 TRP A 196 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00286 (16128) covalent geometry : angle 0.48173 (21627) SS BOND : bond 0.00095 ( 4) SS BOND : angle 0.23615 ( 8) hydrogen bonds : bond 0.04475 ( 1197) hydrogen bonds : angle 3.58440 ( 3540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7080.74 seconds wall clock time: 121 minutes 5.72 seconds (7265.72 seconds total)