Starting phenix.real_space_refine on Tue Dec 31 15:43:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyd_18751/12_2024/8qyd_18751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyd_18751/12_2024/8qyd_18751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyd_18751/12_2024/8qyd_18751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyd_18751/12_2024/8qyd_18751.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyd_18751/12_2024/8qyd_18751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyd_18751/12_2024/8qyd_18751.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 49 5.16 5 C 10318 2.51 5 N 2515 2.21 5 O 3248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16150 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2231 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 271} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 271} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2260 Chain: "B" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 271} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 270} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 271} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 271} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain: "G" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {' CA': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 203 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 12.89, per 1000 atoms: 0.80 Number of scatterers: 16150 At special positions: 0 Unit cell: (83.2, 80.704, 248.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 49 16.00 P 15 15.00 O 3248 8.00 N 2515 7.00 C 10318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 86 " distance=2.03 Simple disulfide: pdb=" SG CYS F 165 " - pdb=" SG CYS F 240 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 86 " distance=2.03 Simple disulfide: pdb=" SG CYS G 165 " - pdb=" SG CYS G 240 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 7 sheets defined 78.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 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: 4.79 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2509 1.31 - 1.44: 4155 1.44 - 1.56: 9233 1.56 - 1.69: 136 1.69 - 1.82: 95 Bond restraints: 16128 Sorted by residual: bond pdb=" C38 PEE B 803 " pdb=" C39 PEE B 803 " ideal model delta sigma weight residual 1.523 1.353 0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" C38 PEE C 802 " pdb=" C39 PEE C 802 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.18e+01 bond pdb=" C38 PEE D 802 " pdb=" C39 PEE D 802 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.17e+01 bond pdb=" C38 PEE E 802 " pdb=" C39 PEE E 802 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C38 PEE B 801 " pdb=" C39 PEE B 801 " ideal model delta sigma weight residual 1.523 1.355 0.168 2.00e-02 2.50e+03 7.09e+01 ... (remaining 16123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.42: 21596 10.42 - 20.84: 20 20.84 - 31.25: 1 31.25 - 41.67: 0 41.67 - 52.09: 10 Bond angle restraints: 21627 Sorted by residual: angle pdb=" C38 PEE B 801 " pdb=" C39 PEE B 801 " pdb=" C40 PEE B 801 " ideal model delta sigma weight residual 112.47 164.56 -52.09 3.00e+00 1.11e-01 3.01e+02 angle pdb=" C38 PEE D 802 " pdb=" C39 PEE D 802 " pdb=" C40 PEE D 802 " ideal model delta sigma weight residual 112.47 164.55 -52.08 3.00e+00 1.11e-01 3.01e+02 angle pdb=" C38 PEE E 802 " pdb=" C39 PEE E 802 " pdb=" C40 PEE E 802 " ideal model delta sigma weight residual 112.47 164.07 -51.60 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C38 PEE C 802 " pdb=" C39 PEE C 802 " pdb=" C40 PEE C 802 " ideal model delta sigma weight residual 112.47 163.89 -51.42 3.00e+00 1.11e-01 2.94e+02 angle pdb=" C38 PEE B 803 " pdb=" C39 PEE B 803 " pdb=" C40 PEE B 803 " ideal model delta sigma weight residual 112.47 163.82 -51.35 3.00e+00 1.11e-01 2.93e+02 ... (remaining 21622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 9576 33.69 - 67.38: 333 67.38 - 101.07: 36 101.07 - 134.77: 19 134.77 - 168.46: 9 Dihedral angle restraints: 9973 sinusoidal: 4401 harmonic: 5572 Sorted by residual: dihedral pdb=" CD ARG A 77 " pdb=" NE ARG A 77 " pdb=" CZ ARG A 77 " pdb=" NH1 ARG A 77 " ideal model delta sinusoidal sigma weight residual 0.00 -83.11 83.11 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CD ARG B 77 " pdb=" NE ARG B 77 " pdb=" CZ ARG B 77 " pdb=" NH1 ARG B 77 " ideal model delta sinusoidal sigma weight residual 0.00 -76.34 76.34 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" C ARG B 77 " pdb=" N ARG B 77 " pdb=" CA ARG B 77 " pdb=" CB ARG B 77 " ideal model delta harmonic sigma weight residual -122.60 -140.07 17.47 0 2.50e+00 1.60e-01 4.88e+01 ... (remaining 9970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2362 0.115 - 0.230: 22 0.230 - 0.345: 0 0.345 - 0.460: 0 0.460 - 0.575: 6 Chirality restraints: 2390 Sorted by residual: chirality pdb=" C2 PEE B 803 " pdb=" C1 PEE B 803 " pdb=" C3 PEE B 803 " pdb=" O2 PEE B 803 " both_signs ideal model delta sigma weight residual False -2.33 -2.90 0.58 2.00e-01 2.50e+01 8.27e+00 chirality pdb=" C2 PEE E 802 " pdb=" C1 PEE E 802 " pdb=" C3 PEE E 802 " pdb=" O2 PEE E 802 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C2 PEE C 802 " pdb=" C1 PEE C 802 " pdb=" C3 PEE C 802 " pdb=" O2 PEE C 802 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.24e+00 ... (remaining 2387 not shown) Planarity restraints: 2660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 77 " -1.084 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARG A 77 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 77 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 77 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 77 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 77 " 1.073 9.50e-02 1.11e+02 4.81e-01 1.39e+02 pdb=" NE ARG B 77 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 77 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 77 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 77 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 77 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ARG A 77 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG A 77 " -0.024 2.00e-02 2.50e+03 pdb=" N SER A 78 " -0.023 2.00e-02 2.50e+03 ... (remaining 2657 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 450 2.70 - 3.25: 15856 3.25 - 3.80: 27534 3.80 - 4.35: 34858 4.35 - 4.90: 59157 Nonbonded interactions: 137855 Sorted by model distance: nonbonded pdb=" OE1 GLU F 95 " pdb=" NE ARG F 98 " model vdw 2.152 3.120 nonbonded pdb=" OE1 GLU A 210 " pdb=" O HOH A 901 " model vdw 2.161 3.040 nonbonded pdb=" N LEU A 80 " pdb=" O HOH A 902 " model vdw 2.167 3.120 nonbonded pdb="CA CA E 803 " pdb=" O HOH A 906 " model vdw 2.167 2.510 nonbonded pdb=" OH TYR E 208 " pdb=" OA4 CDL E 801 " model vdw 2.172 3.040 ... (remaining 137850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 174 or resid 176 through 280)) selection = (chain 'B' and (resid 1 through 174 or resid 176 through 280)) selection = (chain 'C' and (resid 1 through 174 or resid 176 through 280)) selection = (chain 'D' and (resid 1 through 174 or resid 176 through 280)) selection = (chain 'E' and (resid 1 through 174 or resid 176 through 280)) } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 40.360 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 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:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 16128 Z= 0.535 Angle : 1.365 52.091 21627 Z= 0.531 Chirality : 0.048 0.575 2390 Planarity : 0.014 0.486 2660 Dihedral : 18.408 168.458 6337 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.52 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.19), residues: 1880 helix: 3.23 (0.13), residues: 1280 sheet: -0.45 (0.78), residues: 50 loop : -0.31 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 PHE 0.016 0.002 PHE G 217 TYR 0.017 0.001 TYR D 208 ARG 0.008 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7499 (mp0) cc_final: 0.7284 (mp0) REVERT: B 96 GLU cc_start: 0.6549 (pt0) cc_final: 0.6209 (pt0) REVERT: D 44 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7858 (mtm110) REVERT: D 69 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7252 (mm-30) REVERT: D 234 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7639 (ttmt) REVERT: E 81 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8156 (ttpm) REVERT: E 103 LYS cc_start: 0.8157 (ptmm) cc_final: 0.7953 (ptmt) REVERT: E 175 ARG cc_start: 0.8035 (ttp-110) cc_final: 0.7794 (ttp-110) REVERT: F 58 LYS cc_start: 0.7113 (ttpt) cc_final: 0.6859 (tttp) REVERT: F 217 PHE cc_start: 0.5851 (m-80) cc_final: 0.5344 (m-10) REVERT: G 76 ARG cc_start: 0.3182 (mmp80) cc_final: 0.2835 (mtm180) REVERT: G 213 ARG cc_start: 0.5528 (tmt170) cc_final: 0.5145 (tpt90) outliers start: 2 outliers final: 0 residues processed: 216 average time/residue: 1.6870 time to fit residues: 396.7794 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 : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 234 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 3.9990 chunk 142 optimal weight: 0.0980 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN D 134 HIS E 5 ASN F 158 GLN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN G 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16128 Z= 0.200 Angle : 0.508 7.638 21627 Z= 0.261 Chirality : 0.038 0.155 2390 Planarity : 0.004 0.059 2660 Dihedral : 18.323 178.119 2751 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.91 % Allowed : 6.60 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.19), residues: 1880 helix: 3.50 (0.13), residues: 1283 sheet: -0.42 (0.83), residues: 48 loop : -0.36 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 196 HIS 0.005 0.001 HIS A 92 PHE 0.011 0.001 PHE E 75 TYR 0.018 0.001 TYR E 208 ARG 0.007 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7542 (mtpp) REVERT: B 96 GLU cc_start: 0.6545 (pt0) cc_final: 0.6233 (pt0) REVERT: C 69 GLU cc_start: 0.8115 (tp30) cc_final: 0.7783 (tp30) REVERT: D 69 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7286 (mm-30) REVERT: E 81 LYS cc_start: 0.8350 (ttpt) cc_final: 0.8101 (ttpt) REVERT: E 103 LYS cc_start: 0.8166 (ptmm) cc_final: 0.7898 (ptmt) REVERT: E 175 ARG cc_start: 0.8019 (ttp-110) cc_final: 0.7786 (ttp-110) REVERT: F 12 ARG cc_start: 0.5236 (tmt170) cc_final: 0.4429 (tmm160) REVERT: F 95 GLU cc_start: 0.5907 (tp30) cc_final: 0.5408 (pm20) REVERT: F 217 PHE cc_start: 0.5776 (m-80) cc_final: 0.5259 (m-10) outliers start: 15 outliers final: 7 residues processed: 181 average time/residue: 1.5438 time to fit residues: 306.1335 Evaluate side-chains 165 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 171 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS B 156 ASN E 5 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16128 Z= 0.301 Angle : 0.522 7.331 21627 Z= 0.271 Chirality : 0.040 0.161 2390 Planarity : 0.004 0.062 2660 Dihedral : 17.866 178.134 2747 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.39 % Allowed : 8.12 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.19), residues: 1880 helix: 3.36 (0.13), residues: 1290 sheet: -0.57 (0.80), residues: 53 loop : -0.45 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 196 HIS 0.005 0.001 HIS D 82 PHE 0.014 0.002 PHE E 181 TYR 0.024 0.002 TYR E 208 ARG 0.007 0.001 ARG B 244 *********************** 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 186 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.898 Fit side-chains REVERT: A 103 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7517 (mtpp) REVERT: B 96 GLU cc_start: 0.6755 (pt0) cc_final: 0.6380 (pt0) REVERT: C 7 ILE cc_start: 0.7897 (mp) cc_final: 0.7679 (mp) REVERT: D 69 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7193 (mm-30) REVERT: E 121 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: F 12 ARG cc_start: 0.5264 (tmt170) cc_final: 0.4538 (tmm160) REVERT: G 111 GLN cc_start: 0.2361 (OUTLIER) cc_final: 0.1912 (pt0) outliers start: 23 outliers final: 12 residues processed: 176 average time/residue: 1.6203 time to fit residues: 313.0170 Evaluate side-chains 166 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 111 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 171 optimal weight: 0.2980 chunk 181 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 0.0670 chunk 48 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16128 Z= 0.174 Angle : 0.456 8.170 21627 Z= 0.237 Chirality : 0.036 0.163 2390 Planarity : 0.004 0.058 2660 Dihedral : 17.184 178.803 2747 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.51 % Allowed : 9.57 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.19), residues: 1880 helix: 3.63 (0.13), residues: 1305 sheet: -0.32 (0.85), residues: 46 loop : -0.42 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 196 HIS 0.003 0.000 HIS D 82 PHE 0.027 0.001 PHE F 217 TYR 0.018 0.001 TYR E 208 ARG 0.009 0.000 ARG E 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.909 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7515 (mtpp) REVERT: B 96 GLU cc_start: 0.6722 (pt0) cc_final: 0.6377 (pt0) REVERT: C 7 ILE cc_start: 0.7961 (mp) cc_final: 0.7734 (mp) REVERT: C 69 GLU cc_start: 0.8066 (tp30) cc_final: 0.7762 (tp30) REVERT: C 248 GLU cc_start: 0.6234 (mt-10) cc_final: 0.5860 (mt-10) REVERT: D 54 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7728 (mtp180) REVERT: D 69 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7176 (mm-30) REVERT: D 121 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: F 12 ARG cc_start: 0.5310 (tmt170) cc_final: 0.4865 (tmm160) REVERT: F 217 PHE cc_start: 0.5516 (m-80) cc_final: 0.5065 (m-10) REVERT: G 12 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.5785 (tpp-160) REVERT: G 111 GLN cc_start: 0.2365 (OUTLIER) cc_final: 0.1922 (pt0) outliers start: 25 outliers final: 10 residues processed: 185 average time/residue: 1.5032 time to fit residues: 305.7871 Evaluate side-chains 170 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 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 E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 111 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN D 120 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16128 Z= 0.253 Angle : 0.501 13.049 21627 Z= 0.257 Chirality : 0.038 0.204 2390 Planarity : 0.004 0.059 2660 Dihedral : 17.119 178.967 2747 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.51 % Allowed : 10.78 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.19), residues: 1880 helix: 3.50 (0.13), residues: 1287 sheet: -0.37 (0.86), residues: 46 loop : -0.37 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 PHE 0.019 0.002 PHE F 217 TYR 0.020 0.001 TYR E 208 ARG 0.007 0.000 ARG B 244 *********************** 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: 25 poor density : 161 time to evaluate : 1.785 Fit side-chains REVERT: A 103 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7549 (mtpp) REVERT: B 96 GLU cc_start: 0.6800 (pt0) cc_final: 0.6377 (pt0) REVERT: C 7 ILE cc_start: 0.7868 (mp) cc_final: 0.7615 (mp) REVERT: C 248 GLU cc_start: 0.6278 (mt-10) cc_final: 0.5971 (mt-10) REVERT: D 54 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7619 (mtp180) REVERT: D 121 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: E 121 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: F 12 ARG cc_start: 0.5300 (tmt170) cc_final: 0.4832 (tmm160) REVERT: F 217 PHE cc_start: 0.5712 (m-80) cc_final: 0.5207 (m-10) REVERT: G 12 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.5765 (tpp-160) REVERT: G 111 GLN cc_start: 0.2205 (OUTLIER) cc_final: 0.1747 (pt0) REVERT: G 167 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5894 (mm) outliers start: 25 outliers final: 10 residues processed: 176 average time/residue: 1.6259 time to fit residues: 314.3779 Evaluate side-chains 169 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 111 GLN Chi-restraints excluded: chain G residue 167 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 181 optimal weight: 0.5980 chunk 150 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16128 Z= 0.197 Angle : 0.482 13.600 21627 Z= 0.246 Chirality : 0.037 0.174 2390 Planarity : 0.004 0.060 2660 Dihedral : 16.795 179.614 2747 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.51 % Allowed : 11.21 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.19), residues: 1880 helix: 3.63 (0.13), residues: 1305 sheet: -0.16 (0.88), residues: 46 loop : -0.37 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.017 0.001 PHE F 217 TYR 0.019 0.001 TYR E 208 ARG 0.008 0.000 ARG E 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.929 Fit side-chains REVERT: A 103 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7565 (mtpp) REVERT: B 96 GLU cc_start: 0.6798 (pt0) cc_final: 0.6403 (pt0) REVERT: C 7 ILE cc_start: 0.7862 (mp) cc_final: 0.7600 (mp) REVERT: C 69 GLU cc_start: 0.8081 (tp30) cc_final: 0.7791 (tp30) REVERT: C 248 GLU cc_start: 0.6264 (mt-10) cc_final: 0.6001 (mt-10) REVERT: D 54 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7702 (mtp180) REVERT: D 69 GLU cc_start: 0.8110 (pt0) cc_final: 0.7601 (mm-30) REVERT: D 121 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: E 121 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: F 12 ARG cc_start: 0.5223 (tmt170) cc_final: 0.4757 (tmm160) REVERT: F 217 PHE cc_start: 0.5793 (m-80) cc_final: 0.5205 (m-10) REVERT: G 12 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5800 (tpp-160) REVERT: G 111 GLN cc_start: 0.2566 (OUTLIER) cc_final: 0.2351 (tt0) REVERT: G 167 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5793 (mm) outliers start: 25 outliers final: 10 residues processed: 178 average time/residue: 1.6496 time to fit residues: 321.6622 Evaluate side-chains 169 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 111 GLN Chi-restraints excluded: chain G residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 153 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16128 Z= 0.205 Angle : 0.481 12.294 21627 Z= 0.247 Chirality : 0.037 0.178 2390 Planarity : 0.004 0.062 2660 Dihedral : 16.440 179.344 2747 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.33 % Allowed : 11.69 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.19), residues: 1880 helix: 3.63 (0.13), residues: 1304 sheet: -0.28 (0.99), residues: 36 loop : -0.32 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.017 0.001 PHE F 217 TYR 0.019 0.001 TYR E 208 ARG 0.009 0.000 ARG E 244 *********************** 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 184 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.937 Fit side-chains REVERT: A 103 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7557 (mtpp) REVERT: B 96 GLU cc_start: 0.6788 (pt0) cc_final: 0.6395 (pt0) REVERT: C 7 ILE cc_start: 0.7845 (mp) cc_final: 0.7592 (mp) REVERT: C 69 GLU cc_start: 0.8085 (tp30) cc_final: 0.7742 (tp30) REVERT: C 248 GLU cc_start: 0.6263 (mt-10) cc_final: 0.5999 (mt-10) REVERT: D 54 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7745 (mtp180) REVERT: D 60 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7186 (mt-10) REVERT: D 69 GLU cc_start: 0.8096 (pt0) cc_final: 0.7585 (mm-30) REVERT: D 121 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8646 (tt0) REVERT: E 79 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6510 (pt0) REVERT: E 121 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: F 12 ARG cc_start: 0.5260 (tmt170) cc_final: 0.4761 (tmm160) REVERT: F 217 PHE cc_start: 0.5905 (m-80) cc_final: 0.5321 (m-10) REVERT: G 12 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.5795 (tpp-160) REVERT: G 111 GLN cc_start: 0.2358 (OUTLIER) cc_final: 0.2084 (pt0) outliers start: 22 outliers final: 11 residues processed: 176 average time/residue: 1.5577 time to fit residues: 301.6149 Evaluate side-chains 173 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain G residue 12 ARG Chi-restraints excluded: chain G residue 111 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 103 GLN ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16128 Z= 0.217 Angle : 0.491 11.484 21627 Z= 0.252 Chirality : 0.037 0.186 2390 Planarity : 0.004 0.063 2660 Dihedral : 16.305 179.613 2747 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.27 % Allowed : 12.17 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.19), residues: 1880 helix: 3.57 (0.13), residues: 1287 sheet: -0.33 (0.99), residues: 36 loop : -0.30 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.016 0.001 PHE F 217 TYR 0.018 0.001 TYR E 208 ARG 0.011 0.000 ARG E 244 *********************** 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 177 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.749 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7561 (mtpp) REVERT: B 96 GLU cc_start: 0.6800 (pt0) cc_final: 0.6405 (pt0) REVERT: C 7 ILE cc_start: 0.7842 (mp) cc_final: 0.7580 (mp) REVERT: C 69 GLU cc_start: 0.8061 (tp30) cc_final: 0.7719 (tp30) REVERT: C 248 GLU cc_start: 0.6264 (mt-10) cc_final: 0.5999 (mt-10) REVERT: D 54 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7726 (mtp180) REVERT: D 69 GLU cc_start: 0.8115 (pt0) cc_final: 0.7604 (mm-30) REVERT: D 121 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: E 79 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6516 (pt0) REVERT: E 121 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: F 12 ARG cc_start: 0.5242 (tmt170) cc_final: 0.4767 (tmm160) REVERT: G 12 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.5794 (tpp-160) REVERT: G 111 GLN cc_start: 0.2315 (OUTLIER) cc_final: 0.2090 (pt0) outliers start: 21 outliers final: 12 residues processed: 169 average time/residue: 1.5016 time to fit residues: 279.4985 Evaluate side-chains 174 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 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 111 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 0.2980 chunk 132 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16128 Z= 0.320 Angle : 0.543 10.865 21627 Z= 0.279 Chirality : 0.040 0.192 2390 Planarity : 0.004 0.065 2660 Dihedral : 16.656 179.390 2747 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.39 % Allowed : 12.60 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.19), residues: 1880 helix: 3.39 (0.13), residues: 1286 sheet: -0.48 (0.90), residues: 44 loop : -0.26 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 196 HIS 0.004 0.001 HIS A 92 PHE 0.016 0.002 PHE A 181 TYR 0.025 0.002 TYR E 208 ARG 0.011 0.001 ARG E 244 *********************** 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 186 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7528 (mtpp) REVERT: B 96 GLU cc_start: 0.6878 (pt0) cc_final: 0.6414 (pt0) REVERT: B 167 SER cc_start: 0.8768 (m) cc_final: 0.8428 (p) REVERT: C 7 ILE cc_start: 0.7893 (mp) cc_final: 0.7636 (mp) REVERT: C 69 GLU cc_start: 0.8013 (tp30) cc_final: 0.7812 (tp30) REVERT: C 248 GLU cc_start: 0.6309 (mt-10) cc_final: 0.6038 (mt-10) REVERT: D 54 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7733 (mtp180) REVERT: D 60 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7159 (mt-10) REVERT: D 69 GLU cc_start: 0.8125 (pt0) cc_final: 0.7607 (mm-30) REVERT: D 121 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8620 (tt0) REVERT: E 79 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6515 (pt0) REVERT: E 121 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: F 12 ARG cc_start: 0.5221 (tmt170) cc_final: 0.4805 (tmm160) REVERT: F 217 PHE cc_start: 0.5301 (m-10) cc_final: 0.4978 (m-10) REVERT: F 244 MET cc_start: 0.0845 (mmp) cc_final: -0.0673 (ptp) REVERT: G 12 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.5810 (tpp-160) REVERT: G 111 GLN cc_start: 0.2425 (OUTLIER) cc_final: 0.2102 (pt0) outliers start: 23 outliers final: 12 residues processed: 176 average time/residue: 1.4766 time to fit residues: 285.7446 Evaluate side-chains 176 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 1.890 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 198 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain E residue 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 111 GLN Chi-restraints excluded: chain G residue 112 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16128 Z= 0.236 Angle : 0.507 10.585 21627 Z= 0.262 Chirality : 0.038 0.201 2390 Planarity : 0.004 0.065 2660 Dihedral : 16.406 177.844 2747 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.21 % Allowed : 12.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.19), residues: 1880 helix: 3.55 (0.13), residues: 1279 sheet: -0.06 (0.76), residues: 59 loop : -0.27 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.013 0.001 PHE A 181 TYR 0.019 0.001 TYR E 208 ARG 0.012 0.000 ARG E 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 GLU cc_start: 0.6822 (pt0) cc_final: 0.6391 (pt0) REVERT: C 7 ILE cc_start: 0.7876 (mp) cc_final: 0.7617 (mp) REVERT: C 69 GLU cc_start: 0.7981 (tp30) cc_final: 0.7780 (tp30) REVERT: C 248 GLU cc_start: 0.6278 (mt-10) cc_final: 0.5988 (mt-10) REVERT: C 257 MET cc_start: 0.6661 (mtm) cc_final: 0.6422 (mtm) REVERT: D 69 GLU cc_start: 0.8109 (pt0) cc_final: 0.7583 (mm-30) REVERT: D 121 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8681 (tt0) REVERT: E 79 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6552 (pt0) REVERT: E 121 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7851 (mp10) REVERT: F 12 ARG cc_start: 0.5283 (tmt170) cc_final: 0.4778 (tmm160) REVERT: F 217 PHE cc_start: 0.5321 (m-10) cc_final: 0.4972 (m-10) REVERT: F 244 MET cc_start: 0.0871 (mmp) cc_final: -0.0625 (ptp) REVERT: G 12 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.5766 (tpp-160) REVERT: G 111 GLN cc_start: 0.2256 (OUTLIER) cc_final: 0.1982 (pt0) outliers start: 20 outliers final: 11 residues processed: 171 average time/residue: 1.4990 time to fit residues: 283.4457 Evaluate side-chains 175 residues out of total 1679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 241 THR 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 111 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 22 optimal weight: 0.0030 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.186371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112810 restraints weight = 19092.201| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.67 r_work: 0.3074 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 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 = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16128 Z= 0.220 Angle : 0.498 10.224 21627 Z= 0.257 Chirality : 0.038 0.198 2390 Planarity : 0.004 0.065 2660 Dihedral : 16.109 175.798 2747 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.39 % Allowed : 12.96 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.19), residues: 1880 helix: 3.60 (0.13), residues: 1279 sheet: 0.02 (0.78), residues: 59 loop : -0.25 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.013 0.001 PHE A 181 TYR 0.018 0.001 TYR E 208 ARG 0.012 0.000 ARG E 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5782.02 seconds wall clock time: 105 minutes 54.10 seconds (6354.10 seconds total)