Starting phenix.real_space_refine on Fri Jul 3 20:29:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyd_18751/07_2026/8qyd_18751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyd_18751/07_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_18751/07_2026/8qyd_18751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyd_18751/07_2026/8qyd_18751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qyd_18751/07_2026/8qyd_18751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyd_18751/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 100 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 202 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "D" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 169 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CDL': 1, 'PEE': 1, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Chain: "E" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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: 3.74, per 1000 atoms: 0.23 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: 1.52 Conformation dependent library (CDL) restraints added in 513.1 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: 2.80 Time building geometry restraints manager: 1.97 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 3.250 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: 10.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.220 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.510 ------------------------------------------------------------------------------- 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 : 0.601 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: 0.6968 time to fit residues: 163.8055 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 : 0.462 ------------------------------------------------------------------------------- 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: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.188173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112185 restraints weight = 23185.466| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.93 r_work: 0.3076 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 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 = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1097 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= 0.153 Angle : 0.522 7.678 21635 Z= 0.268 Chirality : 0.038 0.159 2390 Planarity : 0.004 0.060 2660 Dihedral : 19.661 178.428 2831 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.03 % Allowed : 6.36 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.19), residues: 1880 helix: 3.49 (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 E 75 TRP 0.021 0.002 TRP A 196 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (16128) covalent geometry : angle 0.52164 / 0.27 (21627) SS BOND : bond 0.00185 / 0.09 ( 4) SS BOND : angle 0.70678 / 0.32 ( 8) hydrogen bonds : bond 0.04981 / 3.31 ( 1197) hydrogen bonds : angle 3.81872 / 2.73 ( 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 193 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7545 (mtpp) REVERT: C 69 GLU cc_start: 0.8307 (tp30) cc_final: 0.7984 (tp30) REVERT: D 60 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7294 (mt-10) REVERT: D 69 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7423 (mm-30) REVERT: D 79 GLU cc_start: 0.8206 (pm20) cc_final: 0.7948 (pm20) REVERT: E 81 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8210 (ttpt) REVERT: E 103 LYS cc_start: 0.8194 (ptmm) cc_final: 0.7941 (ptmt) REVERT: E 175 ARG cc_start: 0.8028 (ttp-110) cc_final: 0.7801 (ttp-110) REVERT: E 238 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7377 (mt-10) REVERT: F 12 ARG cc_start: 0.5006 (tmt170) cc_final: 0.4470 (tmm160) REVERT: F 95 GLU cc_start: 0.6123 (tp30) cc_final: 0.5434 (pm20) REVERT: F 217 PHE cc_start: 0.5983 (m-80) cc_final: 0.5609 (m-10) REVERT: G 70 ARG cc_start: 0.1914 (OUTLIER) cc_final: 0.1312 (ptp-170) REVERT: G 76 ARG cc_start: 0.3274 (mmp80) cc_final: 0.3073 (mtm180) REVERT: G 111 GLN cc_start: 0.3457 (mm110) cc_final: 0.2945 (pt0) outliers start: 17 outliers final: 8 residues processed: 188 average time/residue: 0.6631 time to fit residues: 136.5344 Evaluate side-chains 165 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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: 0.7980 chunk 155 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN E 5 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.185126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108180 restraints weight = 27548.177| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.05 r_work: 0.3028 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- 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: 0.8704 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16132 Z= 0.190 Angle : 0.532 13.008 21635 Z= 0.272 Chirality : 0.040 0.162 2390 Planarity : 0.004 0.061 2660 Dihedral : 18.432 178.203 2827 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.39 % Allowed : 8.36 % Favored : 90.25 % 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: 3.42 (0.19), residues: 1880 helix: 3.40 (0.13), residues: 1285 sheet: -0.65 (0.80), residues: 53 loop : -0.39 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 244 TYR 0.025 0.002 TYR E 208 PHE 0.015 0.002 PHE E 181 TRP 0.030 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (16128) covalent geometry : angle 0.53164 / 0.27 (21627) SS BOND : bond 0.00150 / 0.08 ( 4) SS BOND : angle 0.48145 / 0.22 ( 8) hydrogen bonds : bond 0.05249 / 3.48 ( 1197) hydrogen bonds : angle 3.78517 / 2.71 ( 3540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7578 (mtpp) REVERT: C 7 ILE cc_start: 0.8276 (mp) cc_final: 0.8049 (mp) REVERT: D 60 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7328 (mt-10) REVERT: D 69 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7376 (mm-30) REVERT: D 79 GLU cc_start: 0.8200 (pm20) cc_final: 0.7910 (pm20) REVERT: E 121 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: E 257 MET cc_start: 0.7472 (mtp) cc_final: 0.7255 (mtp) REVERT: F 12 ARG cc_start: 0.5118 (tmt170) cc_final: 0.4728 (tmm160) REVERT: G 12 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.5773 (tpp-160) REVERT: G 70 ARG cc_start: 0.1723 (OUTLIER) cc_final: 0.1369 (ptp-170) REVERT: G 111 GLN cc_start: 0.3539 (mm110) cc_final: 0.3159 (pt0) outliers start: 23 outliers final: 12 residues processed: 176 average time/residue: 0.7468 time to fit residues: 143.4868 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 : 0.595 ------------------------------------------------------------------------------- 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 200 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 12 THR 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 12 ARG 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: 0.4980 chunk 124 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 GLN B 156 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 = 0.4122 r_free = 0.4122 target = 0.187291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112278 restraints weight = 25447.517| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.17 r_work: 0.3008 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 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 = 0.2849 r_free = 0.2849 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: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1677 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= 0.145 Angle : 0.484 12.108 21635 Z= 0.248 Chirality : 0.037 0.165 2390 Planarity : 0.004 0.059 2660 Dihedral : 17.579 178.256 2827 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.51 % Allowed : 9.99 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.19), residues: 1880 helix: 3.57 (0.13), residues: 1306 sheet: -0.47 (0.85), residues: 46 loop : -0.45 (0.27), residues: 528 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 0.026 0.001 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 0.00339 / 0.15 (16128) covalent geometry : angle 0.48369 / 0.25 (21627) SS BOND : bond 0.00155 / 0.08 ( 4) SS BOND : angle 0.39016 / 0.17 ( 8) hydrogen bonds : bond 0.04739 / 3.15 ( 1197) hydrogen bonds : angle 3.64599 / 2.62 ( 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 193 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7570 (mtpp) REVERT: C 7 ILE cc_start: 0.8288 (mp) cc_final: 0.8051 (mp) REVERT: C 69 GLU cc_start: 0.8363 (tp30) cc_final: 0.8030 (tp30) REVERT: C 248 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6492 (mt-10) REVERT: D 60 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7253 (mt-10) REVERT: D 69 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7403 (mm-30) REVERT: D 79 GLU cc_start: 0.8223 (pm20) cc_final: 0.7951 (pm20) REVERT: D 121 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: E 79 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6462 (pt0) REVERT: E 121 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: F 12 ARG cc_start: 0.5135 (tmt170) cc_final: 0.4776 (tmm160) REVERT: F 217 PHE cc_start: 0.5817 (m-80) cc_final: 0.5438 (m-10) REVERT: G 111 GLN cc_start: 0.3309 (mm110) cc_final: 0.3044 (pt0) outliers start: 25 outliers final: 11 residues processed: 186 average time/residue: 0.6899 time to fit residues: 140.2158 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 : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 178 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN B 269 ASN D 120 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.186215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110924 restraints weight = 24949.876| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.90 r_work: 0.3022 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 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 = 0.2855 r_free = 0.2855 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: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1775 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 : 0.499 10.445 21635 Z= 0.257 Chirality : 0.038 0.168 2390 Planarity : 0.004 0.059 2660 Dihedral : 17.221 178.415 2827 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.64 % Allowed : 11.21 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z 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: 3.53 (0.19), residues: 1880 helix: 3.49 (0.13), residues: 1287 sheet: -0.40 (0.85), residues: 46 loop : -0.39 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 244 TYR 0.020 0.001 TYR E 208 PHE 0.018 0.002 PHE F 217 TRP 0.030 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (16128) covalent geometry : angle 0.49952 / 0.26 (21627) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 0.40091 / 0.22 ( 8) hydrogen bonds : bond 0.04926 / 3.27 ( 1197) hydrogen bonds : angle 3.67773 / 2.64 ( 3540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.625 Fit side-chains REVERT: A 103 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7577 (mtpp) REVERT: A 120 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: C 7 ILE cc_start: 0.8281 (mp) cc_final: 0.8031 (mp) REVERT: C 248 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6581 (mt-10) REVERT: D 60 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7252 (mt-10) REVERT: D 69 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7358 (mm-30) REVERT: D 79 GLU cc_start: 0.8208 (pm20) cc_final: 0.7990 (pm20) REVERT: D 121 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: E 79 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6472 (pt0) REVERT: E 121 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: E 257 MET cc_start: 0.7275 (mtp) cc_final: 0.6903 (mtm) REVERT: F 12 ARG cc_start: 0.5032 (tmt170) cc_final: 0.4731 (tmm160) REVERT: F 217 PHE cc_start: 0.5875 (m-80) cc_final: 0.5417 (m-10) REVERT: G 190 PHE cc_start: 0.6300 (m-80) cc_final: 0.5090 (m-80) outliers start: 27 outliers final: 12 residues processed: 177 average time/residue: 0.6369 time to fit residues: 123.9045 Evaluate side-chains 170 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 GLN B 156 ASN F 103 GLN G 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.186826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111888 restraints weight = 24759.175| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.89 r_work: 0.3041 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 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 = 0.2869 r_free = 0.2869 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: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16132 Z= 0.149 Angle : 0.487 9.108 21635 Z= 0.251 Chirality : 0.038 0.175 2390 Planarity : 0.004 0.059 2660 Dihedral : 16.851 178.997 2827 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.45 % Allowed : 11.93 % Favored : 86.61 % 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: 3.61 (0.19), residues: 1880 helix: 3.53 (0.13), residues: 1287 sheet: -0.25 (1.00), residues: 36 loop : -0.33 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 244 TYR 0.019 0.001 TYR E 208 PHE 0.018 0.001 PHE F 217 TRP 0.037 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (16128) covalent geometry : angle 0.48686 / 0.25 (21627) SS BOND : bond 0.00108 / 0.05 ( 4) SS BOND : angle 0.34453 / 0.18 ( 8) hydrogen bonds : bond 0.04737 / 3.14 ( 1197) hydrogen bonds : angle 3.63685 / 2.62 ( 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 184 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.576 Fit side-chains REVERT: A 103 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7589 (mtpp) REVERT: C 7 ILE cc_start: 0.8261 (mp) cc_final: 0.8002 (mp) REVERT: C 69 GLU cc_start: 0.8274 (tp30) cc_final: 0.7944 (tp30) REVERT: C 248 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6559 (mt-10) REVERT: D 60 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7211 (mt-10) REVERT: D 69 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7348 (mm-30) REVERT: D 79 GLU cc_start: 0.8184 (pm20) cc_final: 0.7955 (pm20) REVERT: D 121 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8724 (tt0) REVERT: E 79 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6466 (pt0) REVERT: E 121 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: F 217 PHE cc_start: 0.5922 (m-80) cc_final: 0.5408 (m-10) REVERT: G 12 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.5708 (tpp-160) REVERT: G 190 PHE cc_start: 0.6283 (m-80) cc_final: 0.5304 (m-80) outliers start: 24 outliers final: 14 residues processed: 175 average time/residue: 0.6950 time to fit residues: 133.5380 Evaluate side-chains 171 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 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: 4.9990 chunk 39 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 159 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 12 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 GLN B 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.187378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114647 restraints weight = 19424.088| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.87 r_work: 0.3091 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 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 = 0.2895 r_free = 0.2895 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: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2006 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= 0.138 Angle : 0.480 8.265 21635 Z= 0.248 Chirality : 0.037 0.180 2390 Planarity : 0.004 0.062 2660 Dihedral : 16.472 179.979 2827 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.27 % Allowed : 12.36 % Favored : 86.37 % 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: 3.79 (0.19), residues: 1880 helix: 3.66 (0.13), residues: 1304 sheet: -0.21 (0.99), residues: 36 loop : -0.38 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 244 TYR 0.019 0.001 TYR E 208 PHE 0.017 0.001 PHE F 217 TRP 0.034 0.002 TRP A 196 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16128) covalent geometry : angle 0.48004 / 0.25 (21627) SS BOND : bond 0.00129 / 0.06 ( 4) SS BOND : angle 0.25639 / 0.10 ( 8) hydrogen bonds : bond 0.04610 / 3.06 ( 1197) hydrogen bonds : angle 3.59378 / 2.59 ( 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 186 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.639 Fit side-chains REVERT: A 103 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7598 (mtpp) REVERT: C 7 ILE cc_start: 0.8234 (mp) cc_final: 0.7968 (mp) REVERT: C 69 GLU cc_start: 0.8303 (tp30) cc_final: 0.7954 (tp30) REVERT: C 248 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6540 (mt-10) REVERT: D 69 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7387 (mm-30) REVERT: D 79 GLU cc_start: 0.8157 (pm20) cc_final: 0.7947 (pm20) REVERT: D 121 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: E 121 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: F 217 PHE cc_start: 0.6026 (m-80) cc_final: 0.5537 (m-10) REVERT: G 12 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.5761 (tpp-160) REVERT: G 190 PHE cc_start: 0.6318 (m-80) cc_final: 0.5264 (m-80) outliers start: 21 outliers final: 12 residues processed: 177 average time/residue: 0.6418 time to fit residues: 125.2584 Evaluate side-chains 174 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 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 Chi-restraints excluded: chain G residue 214 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 129 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 118 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 166 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.187980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113201 restraints weight = 24742.648| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.88 r_work: 0.3071 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 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 = 0.2889 r_free = 0.2889 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: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2100 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= 0.127 Angle : 0.470 8.664 21635 Z= 0.242 Chirality : 0.036 0.182 2390 Planarity : 0.004 0.062 2660 Dihedral : 16.093 179.216 2827 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.45 % Allowed : 12.66 % Favored : 85.89 % 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: 3.87 (0.19), residues: 1880 helix: 3.74 (0.13), residues: 1302 sheet: -0.17 (1.00), residues: 36 loop : -0.38 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 244 TYR 0.017 0.001 TYR E 208 PHE 0.016 0.001 PHE F 217 TRP 0.034 0.002 TRP A 196 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16128) covalent geometry : angle 0.47029 / 0.24 (21627) SS BOND : bond 0.00088 / 0.04 ( 4) SS BOND : angle 0.27412 / 0.13 ( 8) hydrogen bonds : bond 0.04468 / 2.96 ( 1197) hydrogen bonds : angle 3.55752 / 2.56 ( 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 190 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.536 Fit side-chains REVERT: A 103 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7593 (mtpp) REVERT: C 7 ILE cc_start: 0.8218 (mp) cc_final: 0.7955 (mp) REVERT: C 69 GLU cc_start: 0.8279 (tp30) cc_final: 0.7945 (tp30) REVERT: C 248 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6504 (mt-10) REVERT: D 69 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7366 (mm-30) REVERT: D 79 GLU cc_start: 0.8150 (pm20) cc_final: 0.7916 (pm20) REVERT: D 248 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6530 (mt-10) REVERT: E 79 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6653 (pt0) REVERT: F 217 PHE cc_start: 0.6023 (m-80) cc_final: 0.5519 (m-10) REVERT: G 12 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.5712 (tpp-160) REVERT: G 190 PHE cc_start: 0.6370 (m-80) cc_final: 0.5322 (m-80) outliers start: 24 outliers final: 12 residues processed: 181 average time/residue: 0.5952 time to fit residues: 118.9450 Evaluate side-chains 173 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 C residue 251 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 164 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 174 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 142 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.187913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.115707 restraints weight = 18109.823| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.60 r_work: 0.3131 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16132 Z= 0.124 Angle : 0.477 7.470 21635 Z= 0.245 Chirality : 0.037 0.202 2390 Planarity : 0.004 0.064 2660 Dihedral : 15.835 179.448 2827 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.09 % Allowed : 13.33 % Favored : 85.58 % 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: 3.92 (0.19), residues: 1880 helix: 3.79 (0.13), residues: 1301 sheet: -0.40 (0.98), residues: 38 loop : -0.39 (0.27), residues: 541 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 0.016 0.001 PHE F 217 TRP 0.038 0.002 TRP A 196 HIS 0.002 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (16128) covalent geometry : angle 0.47725 / 0.24 (21627) SS BOND : bond 0.00123 / 0.06 ( 4) SS BOND : angle 0.22405 / 0.10 ( 8) hydrogen bonds : bond 0.04428 / 2.94 ( 1197) hydrogen bonds : angle 3.54381 / 2.56 ( 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 187 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7604 (mtpp) REVERT: B 254 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7212 (mp) REVERT: C 7 ILE cc_start: 0.8217 (mp) cc_final: 0.7956 (mp) REVERT: C 69 GLU cc_start: 0.8179 (tp30) cc_final: 0.7842 (tp30) REVERT: C 248 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6531 (mt-10) REVERT: C 257 MET cc_start: 0.7165 (mtm) cc_final: 0.6953 (mtm) REVERT: D 69 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7364 (mm-30) REVERT: D 79 GLU cc_start: 0.8129 (pm20) cc_final: 0.7908 (pm20) REVERT: D 121 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: D 248 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6562 (mt-10) REVERT: F 217 PHE cc_start: 0.6066 (m-80) cc_final: 0.5566 (m-10) REVERT: G 12 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.5764 (tpp-160) REVERT: G 190 PHE cc_start: 0.6413 (m-80) cc_final: 0.5272 (m-80) outliers start: 18 outliers final: 10 residues processed: 180 average time/residue: 0.6123 time to fit residues: 121.3562 Evaluate side-chains 175 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 123 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.187420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112673 restraints weight = 23161.264| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.82 r_work: 0.3108 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2193 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= 0.145 Angle : 0.496 9.011 21635 Z= 0.254 Chirality : 0.037 0.191 2390 Planarity : 0.004 0.064 2660 Dihedral : 15.802 178.149 2827 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.03 % Allowed : 13.63 % Favored : 85.34 % 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: 3.86 (0.19), residues: 1880 helix: 3.75 (0.13), residues: 1296 sheet: -0.23 (0.87), residues: 48 loop : -0.37 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 244 TYR 0.017 0.001 TYR E 208 PHE 0.015 0.001 PHE F 217 TRP 0.049 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (16128) covalent geometry : angle 0.49640 / 0.25 (21627) SS BOND : bond 0.00075 / 0.04 ( 4) SS BOND : angle 0.26148 / 0.13 ( 8) hydrogen bonds : bond 0.04643 / 3.08 ( 1197) hydrogen bonds : angle 3.59065 / 2.59 ( 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 176 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7636 (mtpp) REVERT: B 60 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7139 (pm20) REVERT: B 254 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7245 (mp) REVERT: C 7 ILE cc_start: 0.8279 (mp) cc_final: 0.8020 (mp) REVERT: C 69 GLU cc_start: 0.8245 (tp30) cc_final: 0.8042 (tp30) REVERT: C 248 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6604 (mt-10) REVERT: D 69 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7469 (mm-30) REVERT: D 79 GLU cc_start: 0.8101 (pm20) cc_final: 0.7877 (pm20) REVERT: D 121 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: D 248 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6619 (mt-10) REVERT: E 121 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: F 217 PHE cc_start: 0.6107 (m-80) cc_final: 0.5611 (m-10) REVERT: F 244 MET cc_start: 0.0872 (mmp) cc_final: -0.0722 (ptp) REVERT: G 12 ARG cc_start: 0.6646 (OUTLIER) cc_final: 0.5812 (tpp-160) REVERT: G 190 PHE cc_start: 0.6400 (m-80) cc_final: 0.5238 (m-80) outliers start: 17 outliers final: 11 residues processed: 170 average time/residue: 0.6165 time to fit residues: 115.4622 Evaluate side-chains 170 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 60 GLU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.187554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.113357 restraints weight = 24454.396| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.22 r_work: 0.3069 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2220 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= 0.144 Angle : 0.496 7.193 21635 Z= 0.255 Chirality : 0.038 0.192 2390 Planarity : 0.004 0.064 2660 Dihedral : 15.699 176.608 2827 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.33 % Allowed : 13.51 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z 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: 3.72 (0.19), residues: 1880 helix: 3.65 (0.13), residues: 1280 sheet: -0.20 (0.88), residues: 48 loop : -0.33 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 244 TYR 0.018 0.001 TYR E 208 PHE 0.015 0.001 PHE F 217 TRP 0.055 0.002 TRP A 196 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (16128) covalent geometry : angle 0.49587 / 0.25 (21627) SS BOND : bond 0.00110 / 0.05 ( 4) SS BOND : angle 0.25054 / 0.13 ( 8) hydrogen bonds : bond 0.04646 / 3.08 ( 1197) hydrogen bonds : angle 3.60704 / 2.60 ( 3540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7268.35 seconds wall clock time: 124 minutes 24.00 seconds (7464.00 seconds total)