Starting phenix.real_space_refine on Thu Aug 6 16:02:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyd_18751/08_2026/8qyd_18751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyd_18751/08_2026/8qyd_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_2026/8qyd_18751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyd_18751/08_2026/8qyd_18751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qyd_18751/08_2026/8qyd_18751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyd_18751/08_2026/8qyd_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 3.85, per 1000 atoms: 0.24 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: 1.23 Conformation dependent library (CDL) restraints added in 662.2 milliseconds 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: 0.38 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: 2.63 Time building geometry restraints manager: 1.65 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: 9535 33.69 - 67.38: 456 67.38 - 101.07: 34 101.07 - 134.77: 19 134.77 - 168.46: 9 Dihedral angle restraints: 10053 sinusoidal: 4481 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 10050 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: 10.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.600 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.009 0.170 16132 Z= 0.448 Angle : 1.398 52.091 21635 Z= 0.540 Chirality : 0.048 0.575 2390 Planarity : 0.014 0.486 2660 Dihedral : 19.508 168.458 6417 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 are 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/Z covalent geometry : bond 0.00899 / 0.45 (16128) covalent geometry : angle 1.39839 / 0.54 (21627) SS BOND : bond 0.00127 / 0.06 ( 4) SS BOND : angle 0.59503 / 0.28 ( 8) hydrogen bonds : bond 0.11035 / 7.49 ( 1197) hydrogen bonds : angle 4.60306 / 3.23 ( 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 : 0.629 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: 0.7662 time to fit residues: 179.9789 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 : 0.663 ------------------------------------------------------------------------------- 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... 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 = 0.4125 r_free = 0.4125 target = 0.187540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111373 restraints weight = 23134.500| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.90 r_work: 0.3048 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 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 = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1078 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= 0.151 Angle : 0.519 7.625 21635 Z= 0.266 Chirality : 0.038 0.153 2390 Planarity : 0.004 0.065 2660 Dihedral : 19.588 177.389 2831 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.97 % Allowed : 6.42 % 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 are not related in a simple way. whole: 3.49 (0.19), residues: 1880 helix: 3.46 (0.13), residues: 1283 sheet: -0.44 (0.83), residues: 48 loop : -0.36 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 244 TYR 0.019 0.001 TYR E 208 PHE 0.012 0.001 PHE F 217 TRP 0.021 0.002 TRP A 196 HIS 0.004 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (16128) covalent geometry : angle 0.51849 / 0.27 (21627) SS BOND : bond 0.00168 / 0.08 ( 4) SS BOND : angle 0.67434 / 0.30 ( 8) hydrogen bonds : bond 0.05011 / 3.32 ( 1197) hydrogen bonds : angle 3.83626 / 2.74 ( 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 191 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7550 (mtpp) REVERT: B 96 GLU cc_start: 0.6853 (pt0) cc_final: 0.6650 (pt0) REVERT: C 69 GLU cc_start: 0.8322 (tp30) cc_final: 0.7998 (tp30) REVERT: D 60 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7366 (mt-10) REVERT: D 69 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7448 (mm-30) REVERT: D 79 GLU cc_start: 0.8221 (pm20) cc_final: 0.7994 (pm20) REVERT: E 81 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8240 (ttpt) REVERT: E 103 LYS cc_start: 0.8190 (ptmm) cc_final: 0.7935 (ptmt) REVERT: E 175 ARG cc_start: 0.8007 (ttp-110) cc_final: 0.7782 (ttp-110) REVERT: E 238 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7397 (mt-10) REVERT: F 12 ARG cc_start: 0.4980 (tmt170) cc_final: 0.4506 (tmm160) REVERT: F 217 PHE cc_start: 0.5990 (m-80) cc_final: 0.5611 (m-10) REVERT: G 70 ARG cc_start: 0.1912 (OUTLIER) cc_final: 0.1311 (ptp-170) REVERT: G 111 GLN cc_start: 0.3489 (mm110) cc_final: 0.2983 (pt0) outliers start: 16 outliers final: 8 residues processed: 186 average time/residue: 0.6352 time to fit residues: 129.4252 Evaluate side-chains 164 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 1.9990 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN E 5 ASN G 48 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 = 0.4108 r_free = 0.4108 target = 0.185949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108369 restraints weight = 28002.013| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.11 r_work: 0.3009 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16132 Z= 0.166 Angle : 0.512 12.553 21635 Z= 0.263 Chirality : 0.039 0.158 2390 Planarity : 0.004 0.060 2660 Dihedral : 18.154 179.106 2827 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.39 % Allowed : 8.30 % Favored : 90.31 % 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 are not related in a simple way. whole: 3.48 (0.19), residues: 1880 helix: 3.44 (0.13), residues: 1284 sheet: -0.48 (0.78), residues: 55 loop : -0.36 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 244 TYR 0.023 0.001 TYR E 208 PHE 0.013 0.002 PHE E 181 TRP 0.029 0.002 TRP A 196 HIS 0.003 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (16128) covalent geometry : angle 0.51219 / 0.26 (21627) SS BOND : bond 0.00147 / 0.07 ( 4) SS BOND : angle 0.41188 / 0.19 ( 8) hydrogen bonds : bond 0.05004 / 3.31 ( 1197) hydrogen bonds : angle 3.73522 / 2.68 ( 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 188 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7584 (mtpp) REVERT: B 96 GLU cc_start: 0.7046 (pt0) cc_final: 0.6783 (pt0) REVERT: C 7 ILE cc_start: 0.8244 (mp) cc_final: 0.8018 (mp) REVERT: D 60 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7351 (mt-10) REVERT: D 69 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7345 (mm-30) REVERT: D 79 GLU cc_start: 0.8198 (pm20) cc_final: 0.7898 (pm20) REVERT: E 121 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: E 257 MET cc_start: 0.7461 (mtp) cc_final: 0.7235 (mtp) REVERT: F 12 ARG cc_start: 0.5170 (tmt170) cc_final: 0.4690 (tmm160) REVERT: G 70 ARG cc_start: 0.1561 (OUTLIER) cc_final: 0.1245 (ptp-170) REVERT: G 111 GLN cc_start: 0.3469 (mm110) cc_final: 0.3085 (pt0) outliers start: 23 outliers final: 10 residues processed: 178 average time/residue: 0.7194 time to fit residues: 140.1168 Evaluate side-chains 165 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 70 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 67 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN D 120 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.186965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111565 restraints weight = 25523.789| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.92 r_work: 0.3063 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 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 = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1663 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= 0.137 Angle : 0.479 12.369 21635 Z= 0.245 Chirality : 0.037 0.161 2390 Planarity : 0.004 0.058 2660 Dihedral : 17.473 178.749 2827 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.45 % Allowed : 9.93 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.19), residues: 1880 helix: 3.58 (0.13), residues: 1306 sheet: -0.49 (0.83), residues: 46 loop : -0.43 (0.27), residues: 528 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 0.026 0.001 PHE F 217 TRP 0.022 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16128) covalent geometry : angle 0.47858 / 0.24 (21627) SS BOND : bond 0.00149 / 0.07 ( 4) SS BOND : angle 0.36384 / 0.15 ( 8) hydrogen bonds : bond 0.04650 / 3.08 ( 1197) hydrogen bonds : angle 3.62978 / 2.61 ( 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 194 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7586 (mtpp) REVERT: B 96 GLU cc_start: 0.7044 (pt0) cc_final: 0.6783 (pt0) REVERT: C 7 ILE cc_start: 0.8293 (mp) cc_final: 0.8060 (mp) REVERT: C 69 GLU cc_start: 0.8310 (tp30) cc_final: 0.7970 (tp30) REVERT: C 248 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6538 (mt-10) REVERT: D 54 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7771 (mtp180) REVERT: D 60 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7262 (mt-10) REVERT: D 69 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7371 (mm-30) REVERT: D 79 GLU cc_start: 0.8212 (pm20) cc_final: 0.7976 (pm20) REVERT: E 121 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: F 12 ARG cc_start: 0.5140 (tmt170) cc_final: 0.4879 (tmm160) REVERT: F 98 ARG cc_start: 0.5470 (pmt-80) cc_final: 0.4597 (ttm110) REVERT: F 217 PHE cc_start: 0.5702 (m-80) cc_final: 0.5297 (m-10) REVERT: G 9 LYS cc_start: 0.6288 (mppt) cc_final: 0.6056 (ttpp) REVERT: G 12 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.5770 (tpp-160) REVERT: G 111 GLN cc_start: 0.3258 (mm110) cc_final: 0.2990 (pt0) outliers start: 24 outliers final: 11 residues processed: 188 average time/residue: 0.6487 time to fit residues: 133.5649 Evaluate side-chains 171 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 54 ARG 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: 9.9990 chunk 133 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 181 optimal weight: 0.0770 chunk 108 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN B 269 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 = 0.4104 r_free = 0.4104 target = 0.185509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110040 restraints weight = 24910.073| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.88 r_work: 0.3006 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1789 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= 0.166 Angle : 0.502 10.314 21635 Z= 0.258 Chirality : 0.038 0.172 2390 Planarity : 0.004 0.059 2660 Dihedral : 17.129 179.163 2827 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.64 % Allowed : 10.42 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.55 (0.19), residues: 1880 helix: 3.49 (0.13), residues: 1284 sheet: 0.00 (0.84), residues: 47 loop : -0.36 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 244 TYR 0.021 0.001 TYR E 208 PHE 0.019 0.002 PHE F 217 TRP 0.024 0.002 TRP A 196 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (16128) covalent geometry : angle 0.50158 / 0.26 (21627) SS BOND : bond 0.00107 / 0.05 ( 4) SS BOND : angle 0.42138 / 0.23 ( 8) hydrogen bonds : bond 0.04945 / 3.28 ( 1197) hydrogen bonds : angle 3.68912 / 2.65 ( 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 189 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.653 Fit side-chains REVERT: A 103 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7583 (mtpp) REVERT: B 96 GLU cc_start: 0.7120 (pt0) cc_final: 0.6806 (pt0) REVERT: C 7 ILE cc_start: 0.8236 (mp) cc_final: 0.7999 (mp) REVERT: C 248 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6540 (mt-10) REVERT: D 54 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7695 (mtp180) REVERT: D 60 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7281 (mt-10) REVERT: D 69 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7366 (mm-30) REVERT: E 121 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: E 257 MET cc_start: 0.7230 (mtp) cc_final: 0.6891 (mtm) REVERT: F 12 ARG cc_start: 0.5047 (tmt170) cc_final: 0.4817 (tmm160) REVERT: F 217 PHE cc_start: 0.5916 (m-80) cc_final: 0.5426 (m-10) REVERT: G 12 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.5722 (tpp-160) REVERT: G 190 PHE cc_start: 0.6299 (m-80) cc_final: 0.5083 (m-80) outliers start: 27 outliers final: 12 residues processed: 181 average time/residue: 0.7067 time to fit residues: 140.2339 Evaluate side-chains 168 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain C residue 251 VAL 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 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: 0.5980 chunk 163 optimal weight: 7.9990 chunk 183 optimal weight: 0.0270 chunk 80 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN G 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.187214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112325 restraints weight = 24713.442| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.84 r_work: 0.3056 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 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 = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16132 Z= 0.128 Angle : 0.472 9.123 21635 Z= 0.243 Chirality : 0.037 0.172 2390 Planarity : 0.004 0.059 2660 Dihedral : 16.606 179.883 2827 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.15 % Allowed : 11.63 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.19), residues: 1880 helix: 3.64 (0.13), residues: 1305 sheet: -0.25 (0.99), residues: 36 loop : -0.34 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 244 TYR 0.016 0.001 TYR E 208 PHE 0.018 0.001 PHE F 217 TRP 0.023 0.002 TRP A 196 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16128) covalent geometry : angle 0.47171 / 0.24 (21627) SS BOND : bond 0.00121 / 0.06 ( 4) SS BOND : angle 0.35301 / 0.18 ( 8) hydrogen bonds : bond 0.04494 / 2.98 ( 1197) hydrogen bonds : angle 3.57745 / 2.58 ( 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 186 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.619 Fit side-chains REVERT: A 103 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7528 (mtpp) REVERT: B 96 GLU cc_start: 0.7092 (pt0) cc_final: 0.6819 (pt0) REVERT: C 7 ILE cc_start: 0.8224 (mp) cc_final: 0.7959 (mp) REVERT: C 69 GLU cc_start: 0.8265 (tp30) cc_final: 0.7947 (tp30) REVERT: C 248 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6517 (mt-10) REVERT: D 60 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7176 (mt-10) REVERT: D 69 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7400 (mm-30) REVERT: F 12 ARG cc_start: 0.5060 (tmt170) cc_final: 0.4843 (tmm160) REVERT: F 217 PHE cc_start: 0.5949 (m-80) cc_final: 0.5465 (m-10) REVERT: G 12 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.5731 (tpp-160) REVERT: G 190 PHE cc_start: 0.6307 (m-80) cc_final: 0.5128 (m-80) outliers start: 19 outliers final: 10 residues processed: 179 average time/residue: 0.6983 time to fit residues: 137.5903 Evaluate side-chains 169 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain 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 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: 9.9990 chunk 39 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 159 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.185671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112088 restraints weight = 18843.422| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.65 r_work: 0.3097 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1988 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= 0.161 Angle : 0.501 8.087 21635 Z= 0.259 Chirality : 0.038 0.179 2390 Planarity : 0.004 0.063 2660 Dihedral : 16.536 178.953 2827 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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 : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.61 (0.19), residues: 1880 helix: 3.53 (0.13), residues: 1286 sheet: -0.41 (0.97), residues: 38 loop : -0.31 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 244 TYR 0.021 0.001 TYR E 208 PHE 0.017 0.002 PHE F 217 TRP 0.039 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (16128) covalent geometry : angle 0.50120 / 0.26 (21627) SS BOND : bond 0.00117 / 0.06 ( 4) SS BOND : angle 0.25814 / 0.11 ( 8) hydrogen bonds : bond 0.04875 / 3.22 ( 1197) hydrogen bonds : angle 3.64825 / 2.62 ( 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 185 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.623 Fit side-chains REVERT: A 103 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7592 (mtpp) REVERT: B 96 GLU cc_start: 0.7131 (pt0) cc_final: 0.6842 (pt0) REVERT: C 7 ILE cc_start: 0.8279 (mp) cc_final: 0.8023 (mp) REVERT: C 69 GLU cc_start: 0.8228 (tp30) cc_final: 0.7832 (tp30) REVERT: C 248 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6584 (mt-10) REVERT: D 69 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7414 (mm-30) REVERT: D 121 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: E 121 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: F 217 PHE cc_start: 0.6014 (m-80) cc_final: 0.5507 (m-10) REVERT: G 12 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.5813 (tpp-160) REVERT: G 190 PHE cc_start: 0.6289 (m-80) cc_final: 0.5270 (m-80) REVERT: G 213 ARG cc_start: 0.4724 (tpt90) cc_final: 0.4404 (tpt90) outliers start: 23 outliers final: 11 residues processed: 176 average time/residue: 0.7018 time to fit residues: 135.5417 Evaluate side-chains 170 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 129 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 166 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN C 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.186289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111374 restraints weight = 24731.123| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.86 r_work: 0.3092 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 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 = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2082 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= 0.133 Angle : 0.480 8.750 21635 Z= 0.248 Chirality : 0.037 0.279 2390 Planarity : 0.004 0.063 2660 Dihedral : 16.207 179.806 2827 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.39 % Allowed : 12.72 % Favored : 85.89 % 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 are not related in a simple way. whole: 3.82 (0.19), residues: 1880 helix: 3.67 (0.13), residues: 1304 sheet: -0.10 (1.00), residues: 36 loop : -0.35 (0.27), residues: 540 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 0.033 0.002 TRP A 196 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (16128) covalent geometry : angle 0.48005 / 0.25 (21627) SS BOND : bond 0.00109 / 0.05 ( 4) SS BOND : angle 0.27346 / 0.12 ( 8) hydrogen bonds : bond 0.04556 / 3.02 ( 1197) hydrogen bonds : angle 3.59020 / 2.59 ( 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 184 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.658 Fit side-chains REVERT: A 103 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7668 (mtpp) REVERT: B 96 GLU cc_start: 0.7145 (pt0) cc_final: 0.6894 (pt0) REVERT: C 7 ILE cc_start: 0.8289 (mp) cc_final: 0.8033 (mp) REVERT: C 69 GLU cc_start: 0.8322 (tp30) cc_final: 0.7991 (tp30) REVERT: C 248 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6682 (mt-10) REVERT: D 69 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7433 (mm-30) REVERT: D 121 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: F 217 PHE cc_start: 0.6102 (m-80) cc_final: 0.5621 (m-10) REVERT: G 12 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.5712 (tpp-160) REVERT: G 190 PHE cc_start: 0.6412 (m-80) cc_final: 0.5323 (m-80) outliers start: 23 outliers final: 13 residues processed: 175 average time/residue: 0.6400 time to fit residues: 123.7396 Evaluate side-chains 171 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 174 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.186307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113045 restraints weight = 17825.621| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.60 r_work: 0.3086 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16132 Z= 0.149 Angle : 0.494 7.257 21635 Z= 0.255 Chirality : 0.038 0.191 2390 Planarity : 0.004 0.064 2660 Dihedral : 16.069 178.639 2827 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.45 % Allowed : 13.26 % Favored : 85.28 % 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 are not related in a simple way. whole: 3.70 (0.19), residues: 1880 helix: 3.63 (0.13), residues: 1279 sheet: -0.29 (0.87), residues: 48 loop : -0.30 (0.26), residues: 553 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 0.036 0.002 TRP A 196 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (16128) covalent geometry : angle 0.49381 / 0.25 (21627) SS BOND : bond 0.00104 / 0.05 ( 4) SS BOND : angle 0.26194 / 0.12 ( 8) hydrogen bonds : bond 0.04703 / 3.11 ( 1197) hydrogen bonds : angle 3.61074 / 2.60 ( 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 183 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.660 Fit side-chains REVERT: A 103 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7570 (mtpp) REVERT: B 96 GLU cc_start: 0.7103 (pt0) cc_final: 0.6834 (pt0) REVERT: B 254 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7245 (mp) REVERT: C 7 ILE cc_start: 0.8232 (mp) cc_final: 0.7974 (mp) REVERT: C 248 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6560 (mt-10) REVERT: D 69 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7283 (mm-30) REVERT: D 121 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: E 121 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8210 (mp10) REVERT: F 217 PHE cc_start: 0.6054 (m-80) cc_final: 0.5495 (m-10) REVERT: F 244 MET cc_start: 0.0628 (mmp) cc_final: -0.0676 (ptp) REVERT: G 12 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5726 (tpp-160) REVERT: G 190 PHE cc_start: 0.6394 (m-80) cc_final: 0.5321 (m-80) REVERT: G 197 PHE cc_start: 0.4494 (m-80) cc_final: 0.2990 (t80) outliers start: 24 outliers final: 14 residues processed: 173 average time/residue: 0.6661 time to fit residues: 127.1370 Evaluate side-chains 173 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 241 THR 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 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: 1.9990 chunk 82 optimal weight: 9.9990 chunk 106 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.186262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112020 restraints weight = 23187.598| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.16 r_work: 0.3047 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 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 = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16132 Z= 0.150 Angle : 0.504 9.108 21635 Z= 0.258 Chirality : 0.038 0.194 2390 Planarity : 0.004 0.064 2660 Dihedral : 15.960 177.176 2827 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.15 % Allowed : 13.45 % Favored : 85.40 % 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 are not related in a simple way. whole: 3.69 (0.19), residues: 1880 helix: 3.61 (0.13), residues: 1280 sheet: -0.21 (0.88), residues: 48 loop : -0.29 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 244 TYR 0.019 0.001 TYR E 208 PHE 0.016 0.001 PHE F 217 TRP 0.042 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (16128) covalent geometry : angle 0.50416 / 0.26 (21627) SS BOND : bond 0.00145 / 0.07 ( 4) SS BOND : angle 0.31397 / 0.16 ( 8) hydrogen bonds : bond 0.04710 / 3.12 ( 1197) hydrogen bonds : angle 3.63611 / 2.62 ( 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 178 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.610 Fit side-chains REVERT: B 96 GLU cc_start: 0.7176 (pt0) cc_final: 0.6888 (pt0) REVERT: B 254 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7258 (mp) REVERT: C 7 ILE cc_start: 0.8277 (mp) cc_final: 0.8018 (mp) REVERT: C 69 GLU cc_start: 0.8260 (tp30) cc_final: 0.7970 (tp30) REVERT: C 248 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6620 (mt-10) REVERT: C 257 MET cc_start: 0.7149 (mtm) cc_final: 0.6825 (mtm) REVERT: D 69 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7382 (mm-30) REVERT: D 121 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: E 121 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8281 (mp10) REVERT: F 217 PHE cc_start: 0.6055 (m-80) cc_final: 0.5547 (m-10) REVERT: F 244 MET cc_start: 0.1000 (mmp) cc_final: -0.0601 (ptp) REVERT: G 12 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.5705 (tpp-160) REVERT: G 190 PHE cc_start: 0.6421 (m-80) cc_final: 0.5210 (m-80) REVERT: G 197 PHE cc_start: 0.4240 (m-80) cc_final: 0.2745 (t80) outliers start: 19 outliers final: 14 residues processed: 170 average time/residue: 0.6215 time to fit residues: 116.7277 Evaluate side-chains 174 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 B residue 241 THR 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 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 61 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 chunk 112 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 151 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.187415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113009 restraints weight = 24499.765| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.20 r_work: 0.3029 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 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 = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2226 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 : 0.479 7.796 21635 Z= 0.247 Chirality : 0.037 0.192 2390 Planarity : 0.004 0.064 2660 Dihedral : 15.674 175.469 2827 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.09 % Allowed : 13.57 % 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 are not related in a simple way. whole: 3.90 (0.19), residues: 1880 helix: 3.76 (0.13), residues: 1297 sheet: -0.20 (0.88), residues: 48 loop : -0.32 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 244 TYR 0.016 0.001 TYR E 208 PHE 0.015 0.001 PHE F 217 TRP 0.044 0.002 TRP A 196 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16128) covalent geometry : angle 0.47938 / 0.25 (21627) SS BOND : bond 0.00095 / 0.05 ( 4) SS BOND : angle 0.24515 / 0.11 ( 8) hydrogen bonds : bond 0.04447 / 2.95 ( 1197) hydrogen bonds : angle 3.54788 / 2.56 ( 3540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7362.00 seconds wall clock time: 125 minutes 54.72 seconds (7554.72 seconds total)