Starting phenix.real_space_refine on Sat Aug 23 15:13:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5m_61146/08_2025/9j5m_61146.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5m_61146/08_2025/9j5m_61146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j5m_61146/08_2025/9j5m_61146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5m_61146/08_2025/9j5m_61146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j5m_61146/08_2025/9j5m_61146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5m_61146/08_2025/9j5m_61146.map" } resolution = 3.94 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= 0.001 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8168 2.51 5 N 2184 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12892 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1399 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 192} Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 11, 'HIS:plan': 3, 'TYR:plan': 3, 'PHE:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 137 Chain: "B" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1732 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 12, 'TRANS': 217} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1579 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1607 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "G" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1563 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 12, 'TRANS': 201} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "H" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1585 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 193} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1799 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 216} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.96, per 1000 atoms: 0.23 Number of scatterers: 12892 At special positions: 0 Unit cell: (156.2, 193.6, 137.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2478 8.00 N 2184 7.00 C 8168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 210 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 191 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 191 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 191 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.04 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: 0.89 Conformation dependent library (CDL) restraints added in 533.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 40 sheets defined 5.3% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 removed outlier: 4.585A pdb=" N ASN A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 59 through 63' Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.831A pdb=" N VAL A 189 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.662A pdb=" N PHE A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.800A pdb=" N ILE B 92 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.680A pdb=" N LYS B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.853A pdb=" N GLY B 220 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.603A pdb=" N ASP C 91 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER C 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 92' Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 209 through 214 removed outlier: 4.175A pdb=" N PHE D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG D 214 " --> pdb=" O ASP D 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 209 through 214' Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'G' and resid 75 through 77 No H-bonds generated for 'chain 'G' and resid 75 through 77' Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.840A pdb=" N ILE I 92 " --> pdb=" O LYS I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 146 removed outlier: 3.796A pdb=" N LYS I 145 " --> pdb=" O ILE I 141 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU I 146 " --> pdb=" O ALA I 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 141 through 146' Processing helix chain 'I' and resid 202 through 206 removed outlier: 4.255A pdb=" N ASP I 205 " --> pdb=" O GLU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 221 removed outlier: 3.536A pdb=" N VAL I 221 " --> pdb=" O LYS I 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.903A pdb=" N ALA A 19 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 79 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS A 23 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A 75 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 14 removed outlier: 6.387A pdb=" N VAL A 11 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLU A 118 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 13 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 35 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ARG A 51 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP A 37 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 47 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 134 removed outlier: 5.351A pdb=" N ALA A 139 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLY A 181 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU A 141 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS A 179 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS A 143 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA A 177 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 134 removed outlier: 5.351A pdb=" N ALA A 139 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLY A 181 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU A 141 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS A 179 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LYS A 143 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA A 177 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 166 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 155 removed outlier: 3.525A pdb=" N THR A 190 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS A 195 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.566A pdb=" N THR B 79 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 5.896A pdb=" N SER B 11 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 119 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 93 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG B 39 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE B 48 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 51 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 5.896A pdb=" N SER B 11 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 119 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 93 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 137 removed outlier: 3.758A pdb=" N LEU B 153 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 154 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 133 through 137 removed outlier: 3.758A pdb=" N LEU B 153 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS B 154 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET B 192 " --> pdb=" O MET B 185 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET B 185 " --> pdb=" O MET B 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AB3, first strand: chain 'B' and resid 165 through 170 removed outlier: 3.588A pdb=" N HIS B 167 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS B 208 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.218A pdb=" N ALA C 81 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 13 removed outlier: 3.568A pdb=" N ASN C 48 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER C 40 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL C 46 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL C 49 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.525A pdb=" N ALA C 177 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 179 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 133 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N TYR C 173 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.525A pdb=" N ALA C 177 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 179 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 133 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY C 127 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU C 136 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL C 125 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL C 123 " --> pdb=" O ARG C 138 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 207 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 125 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR D 192 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN D 147 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 147 through 151 removed outlier: 3.778A pdb=" N SER C 190 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL C 189 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 202 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 200 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU D 121 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU D 121 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N THR D 140 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL D 123 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ARG D 138 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL D 125 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU D 136 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY D 127 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N HIS D 134 " --> pdb=" O MET D 181 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N MET D 181 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLU D 136 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL D 179 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ARG D 138 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA D 177 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THR D 140 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 175 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 161 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 147 through 151 removed outlier: 3.778A pdb=" N SER C 190 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL C 189 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 202 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 200 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU D 121 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU D 121 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N THR D 140 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL D 123 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ARG D 138 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL D 125 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU D 136 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY D 127 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N HIS D 134 " --> pdb=" O MET D 181 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N MET D 181 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLU D 136 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL D 179 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ARG D 138 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA D 177 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N THR D 140 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 175 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D 166 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.636A pdb=" N GLY D 74 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA D 81 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG D 72 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG D 83 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE D 70 " --> pdb=" O ARG D 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 11 through 13 removed outlier: 3.657A pdb=" N ALA D 13 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 56 removed outlier: 4.467A pdb=" N VAL D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR D 98 " --> pdb=" O LYS D 37 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU D 106 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.526A pdb=" N ILE E 3 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR E 19 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA E 81 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR E 69 " --> pdb=" O VAL E 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.291A pdb=" N ILE E 11 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA E 115 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA E 13 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG E 96 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE E 39 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL E 36 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 48 " --> pdb=" O TRP E 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 125 through 128 removed outlier: 6.412A pdb=" N ARG E 134 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL E 179 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL E 175 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ARG E 140 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N THR E 177 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE E 138 " --> pdb=" O THR E 177 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 125 through 128 removed outlier: 6.412A pdb=" N ARG E 134 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL E 179 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET E 174 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET E 166 " --> pdb=" O MET E 174 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS E 162 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 157 through 158 removed outlier: 4.501A pdb=" N TRP E 150 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.941A pdb=" N CYS G 23 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL G 80 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA G 81 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL G 71 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 11 through 14 removed outlier: 3.596A pdb=" N VAL G 113 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA G 108 " --> pdb=" O CYS G 97 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY G 93 " --> pdb=" O LEU G 112 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG G 96 " --> pdb=" O PHE G 39 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE G 39 " --> pdb=" O ARG G 96 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR G 50 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE G 48 " --> pdb=" O TRP G 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 122 through 128 removed outlier: 6.752A pdb=" N ARG G 134 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE G 181 " --> pdb=" O ILE G 133 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR G 177 " --> pdb=" O CYS G 137 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER G 139 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET G 166 " --> pdb=" O MET G 174 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS G 162 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 147 through 151 removed outlier: 3.514A pdb=" N CYS G 191 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER G 204 " --> pdb=" O CYS G 191 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 193 " --> pdb=" O LYS G 202 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.939A pdb=" N GLY H 88 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE H 35 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ARG H 51 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.939A pdb=" N GLY H 88 " --> pdb=" O VAL H 115 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 21 through 22 removed outlier: 3.579A pdb=" N LEU H 74 " --> pdb=" O ASP H 69 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 130 through 133 removed outlier: 3.853A pdb=" N VAL H 138 " --> pdb=" O GLY H 181 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY H 181 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS H 140 " --> pdb=" O LYS H 179 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS H 179 " --> pdb=" O CYS H 140 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL H 178 " --> pdb=" O ALA H 166 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA H 166 " --> pdb=" O VAL H 178 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.265A pdb=" N SER I 11 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR I 122 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS I 13 " --> pdb=" O THR I 122 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL I 35 " --> pdb=" O SER I 51 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER I 51 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 14 removed outlier: 6.265A pdb=" N SER I 11 " --> pdb=" O ILE I 120 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N THR I 122 " --> pdb=" O SER I 11 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS I 13 " --> pdb=" O THR I 122 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 133 through 135 removed outlier: 3.620A pdb=" N GLU I 157 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU I 155 " --> pdb=" O THR I 135 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN I 180 " --> pdb=" O TRP I 196 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 133 through 135 removed outlier: 3.620A pdb=" N GLU I 157 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU I 155 " --> pdb=" O THR I 135 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 165 through 170 removed outlier: 3.596A pdb=" N LYS I 165 " --> pdb=" O ARG I 213 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN I 169 " --> pdb=" O ARG I 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG I 209 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS I 208 " --> pdb=" O PHE I 227 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN I 223 " --> pdb=" O VAL I 212 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1014 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: 2.10 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4216 1.34 - 1.46: 2621 1.46 - 1.58: 6232 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 13161 Sorted by residual: bond pdb=" CA GLU H 52 " pdb=" CB GLU H 52 " ideal model delta sigma weight residual 1.525 1.548 -0.024 1.36e-02 5.41e+03 3.04e+00 bond pdb=" C SER G 26 " pdb=" N PRO G 27 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.78e+00 bond pdb=" CB GLU H 28 " pdb=" CG GLU H 28 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" CB GLN C 147 " pdb=" CG GLN C 147 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CA LYS A 72 " pdb=" CB LYS A 72 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.54e-02 4.22e+03 1.95e+00 ... (remaining 13156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 17366 2.01 - 4.03: 437 4.03 - 6.04: 77 6.04 - 8.06: 19 8.06 - 10.07: 10 Bond angle restraints: 17909 Sorted by residual: angle pdb=" CA GLU H 52 " pdb=" CB GLU H 52 " pdb=" CG GLU H 52 " ideal model delta sigma weight residual 114.10 124.17 -10.07 2.00e+00 2.50e-01 2.54e+01 angle pdb=" CA LYS D 37 " pdb=" CB LYS D 37 " pdb=" CG LYS D 37 " ideal model delta sigma weight residual 114.10 123.72 -9.62 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA SER G 26 " pdb=" C SER G 26 " pdb=" N PRO G 27 " ideal model delta sigma weight residual 117.69 121.55 -3.86 9.30e-01 1.16e+00 1.72e+01 angle pdb=" CA GLU H 28 " pdb=" CB GLU H 28 " pdb=" CG GLU H 28 " ideal model delta sigma weight residual 114.10 122.35 -8.25 2.00e+00 2.50e-01 1.70e+01 angle pdb=" CA LYS I 158 " pdb=" CB LYS I 158 " pdb=" CG LYS I 158 " ideal model delta sigma weight residual 114.10 122.34 -8.24 2.00e+00 2.50e-01 1.70e+01 ... (remaining 17904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6800 17.88 - 35.77: 870 35.77 - 53.65: 207 53.65 - 71.54: 31 71.54 - 89.42: 14 Dihedral angle restraints: 7922 sinusoidal: 2961 harmonic: 4961 Sorted by residual: dihedral pdb=" CA TYR H 146 " pdb=" C TYR H 146 " pdb=" N PRO H 147 " pdb=" CA PRO H 147 " ideal model delta harmonic sigma weight residual -180.00 -123.52 -56.48 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA SER G 44 " pdb=" C SER G 44 " pdb=" N PRO G 45 " pdb=" CA PRO G 45 " ideal model delta harmonic sigma weight residual 180.00 124.99 55.01 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA SER G 26 " pdb=" C SER G 26 " pdb=" N PRO G 27 " pdb=" CA PRO G 27 " ideal model delta harmonic sigma weight residual -180.00 -132.11 -47.89 0 5.00e+00 4.00e-02 9.17e+01 ... (remaining 7919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1699 0.062 - 0.123: 346 0.123 - 0.185: 18 0.185 - 0.246: 1 0.246 - 0.308: 1 Chirality restraints: 2065 Sorted by residual: chirality pdb=" CB VAL G 71 " pdb=" CA VAL G 71 " pdb=" CG1 VAL G 71 " pdb=" CG2 VAL G 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA GLU H 144 " pdb=" N GLU H 144 " pdb=" C GLU H 144 " pdb=" CB GLU H 144 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE H 55 " pdb=" CA ILE H 55 " pdb=" CG1 ILE H 55 " pdb=" CG2 ILE H 55 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 2062 not shown) Planarity restraints: 2311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR H 146 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO H 147 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO H 147 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO H 147 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 44 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO G 45 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO G 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 45 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 26 " -0.048 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO G 27 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO G 27 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 27 " -0.042 5.00e-02 4.00e+02 ... (remaining 2308 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 826 2.72 - 3.27: 12245 3.27 - 3.81: 19948 3.81 - 4.36: 21772 4.36 - 4.90: 38703 Nonbonded interactions: 93494 Sorted by model distance: nonbonded pdb=" N GLU E 63 " pdb=" OE1 GLU E 63 " model vdw 2.179 3.120 nonbonded pdb=" OD1 ASP H 62 " pdb=" N ASN H 63 " model vdw 2.204 3.120 nonbonded pdb=" OG1 THR A 41 " pdb=" OD1 ASN A 44 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR H 96 " pdb=" OD2 ASP H 105 " model vdw 2.214 3.040 nonbonded pdb=" OG SER C 3 " pdb=" O PHE C 26 " model vdw 2.217 3.040 ... (remaining 93489 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 2 through 150 or (resid 151 through 152 and (name N or nam \ e CA or name C or name O or name CB )) or resid 153 through 159 or (resid 160 th \ rough 162 and (name N or name CA or name C or name O or name CB )) or resid 163 \ through 206)) selection = (chain 'H' and (resid 2 or (resid 3 through 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 6 or (resid 7 through 8 and (name N or \ name CA or name C or name O or name CB )) or resid 9 or (resid 10 and (name N o \ r name CA or name C or name O or name CB )) or resid 11 through 14 or (resid 15 \ and (name N or name CA or name C or name O or name CB )) or resid 16 through 25 \ or (resid 26 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 7 through 33 or (resid 34 and (name N or name CA or name C or name O or name CB \ )) or resid 35 through 51 or (resid 52 and (name N or name CA or name C or name \ O or name CB )) or resid 53 through 59 or (resid 60 through 61 and (name N or na \ me CA or name C or name O or name CB )) or resid 62 or (resid 63 through 64 and \ (name N or name CA or name C or name O or name CB )) or resid 65 through 68 or ( \ resid 69 and (name N or name CA or name C or name O or name CB )) or resid 70 th \ rough 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) o \ r resid 74 through 79 or (resid 80 through 81 and (name N or name CA or name C o \ r name O or name CB )) or resid 82 through 83 or (resid 84 through 87 and (name \ N or name CA or name C or name O or name CB )) or resid 88 through 95 or (resid \ 96 and (name N or name CA or name C or name O or name CB )) or resid 97 through \ 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or resi \ d 100 through 101 or (resid 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 104 or (resid 105 and (name N or name CA or name C \ or name O or name CB )) or resid 106 through 110 or (resid 111 and (name N or n \ ame CA or name C or name O or name CB )) or resid 112 through 113 or (resid 114 \ and (name N or name CA or name C or name O or name CB )) or resid 115 through 11 \ 7 or (resid 118 and (name N or name CA or name C or name O or name CB )) or resi \ d 119 through 129 or (resid 130 and (name N or name CA or name C or name O or na \ me CB )) or resid 131 or (resid 132 through 133 and (name N or name CA or name C \ or name O or name CB )) or resid 134 through 143 or (resid 144 through 145 and \ (name N or name CA or name C or name O or name CB )) or resid 146 through 147 or \ (resid 148 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 9 through 151 or (resid 152 and (name N or name CA or name C or name O or name C \ B )) or resid 153 or (resid 154 and (name N or name CA or name C or name O or na \ me CB )) or resid 155 or (resid 156 and (name N or name CA or name C or name O o \ r name CB )) or resid 157 through 161 or (resid 162 and (name N or name CA or na \ me C or name O or name CB )) or resid 163 through 168 or (resid 169 and (name N \ or name CA or name C or name O or name CB )) or resid 170 through 173 or (resid \ 174 through 175 and (name N or name CA or name C or name O or name CB )) or resi \ d 176 through 178 or (resid 179 through 180 and (name N or name CA or name C or \ name O or name CB )) or resid 181 through 182 or (resid 183 through 186 and (nam \ e N or name CA or name C or name O or name CB )) or resid 187 through 188 or (re \ sid 189 and (name N or name CA or name C or name O or name CB )) or resid 190 th \ rough 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) \ or resid 196 through 200 or (resid 201 and (name N or name CA or name C or name \ O or name CB )) or resid 202 through 205 or (resid 206 and (name N or name CA o \ r name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 2 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 200 or (resid 201 and (name N or na \ me CA or name C or name O or name CB )) or resid 202 through 203 or (resid 204 a \ nd (name N or name CA or name C or name O or name CB )) or resid 205 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 229 or (resid 230 and (name N or name CA or name C or name O or nam \ e CB )))) selection = (chain 'I' and (resid 2 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB )) or resid 23 through 40 or (resid 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 58 or (resid 59 throug \ h 61 and (name N or name CA or name C or name O or name CB )) or resid 62 throug \ h 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) or re \ sid 74 through 102 or (resid 103 and (name N or name CA or name C or name O or n \ ame CB )) or resid 104 through 107 or (resid 108 and (name N or name CA or name \ C or name O or name CB )) or resid 109 through 123 or (resid 124 and (name N or \ name CA or name C or name O or name CB )) or resid 125 through 132 or (resid 133 \ and (name N or name CA or name C or name O or name CB )) or resid 134 through 1 \ 42 or (resid 143 and (name N or name CA or name C or name O or name CB )) or res \ id 144 through 157 or (resid 158 and (name N or name CA or name C or name O or n \ ame CB )) or resid 159 or (resid 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 176 or (resid 177 and (name N or name CA or n \ ame C or name O or name CB )) or resid 178 or (resid 179 and (name N or name CA \ or name C or name O or name CB )) or resid 180 or (resid 181 and (name N or name \ CA or name C or name O or name CB )) or resid 182 through 206 or (resid 207 thr \ ough 209 and (name N or name CA or name C or name O or name CB )) or resid 210 t \ hrough 212 or (resid 213 and (name N or name CA or name C or name O or name CB ) \ ) or resid 214 through 216 or (resid 217 and (name N or name CA or name C or nam \ e O or name CB )) or resid 218 through 230)) } ncs_group { reference = (chain 'C' and (resid 1 through 112 or (resid 113 and (name N or name CA or name \ C or name O or name CB )) or resid 114 through 119 or resid 121 through 123 or \ resid 125 through 127 or (resid 128 and (name N or name CA or name C or name O o \ r name CB )) or resid 130 through 152 or resid 154 through 159 or resid 161 thro \ ugh 173 or resid 175 through 183 or resid 185 through 191 or resid 193 through 1 \ 94 or resid 196 through 215)) selection = (chain 'D' and (resid 1 through 71 or (resid 72 and (name N or name CA or name C \ or name O or name CB )) or resid 73 through 119 or resid 121 through 123 or res \ id 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) or \ resid 127 through 128 or resid 130 through 151 or (resid 152 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 154 and (name N or name CA or n \ ame C or name O or name CB )) or resid 155 or (resid 156 and (name N or name CA \ or name C or name O or name CB )) or resid 157 through 159 or resid 161 through \ 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) or re \ sid 169 through 173 or resid 175 through 180 or (resid 181 through 182 and (name \ N or name CA or name C or name O or name CB )) or resid 183 or resid 185 throug \ h 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) or \ resid 188 through 191 or resid 193 through 194 or resid 196 through 206 or (resi \ d 207 and (name N or name CA or name C or name O or name CB )) or resid 208 thro \ ugh 215)) } ncs_group { reference = (chain 'E' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 through 24 or (resid 25 and (name N or na \ me CA or name C or name O or name CB )) or resid 26 through 29 or (resid 30 thro \ ugh 33 and (name N or name CA or name C or name O or name CB )) or resid 34 thro \ ugh 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or \ resid 51 through 54 or (resid 55 through 56 and (name N or name CA or name C or \ name O or name CB )) or resid 57 through 60 or (resid 61 and (name N or name CA \ or name C or name O or name CB )) or resid 62 or (resid 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 or (resid 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 or (resid 67 and (name N or na \ me CA or name C or name O or name CB )) or resid 68 through 76 or (resid 77 and \ (name N or name CA or name C or name O or name CB )) or resid 78 through 84 or ( \ resid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 th \ rough 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) o \ r resid 96 through 98 or (resid 99 and (name N or name CA or name C or name O or \ name CB )) or resid 100 or (resid 101 and (name N or name CA or name C or name \ O or name CB )) or resid 102 through 144 or (resid 145 and (name N or name CA or \ name C or name O or name CB )) or resid 146 through 203 or (resid 204 and (name \ N or name CA or name C or name O or name CB )) or resid 205 through 215)) selection = (chain 'G' and (resid 2 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 or (resid 58 through 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 153 or (resid 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 182 or \ (resid 183 through 184 and (name N or name CA or name C or name O or name CB )) \ or resid 185 through 200 or (resid 201 and (name N or name CA or name C or name \ O or name CB )) or resid 202 through 215)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.370 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.180 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.003 0.048 13177 Z= 0.146 Angle : 0.777 10.070 17941 Z= 0.414 Chirality : 0.047 0.308 2065 Planarity : 0.005 0.101 2311 Dihedral : 16.642 89.422 4692 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.82 % Favored : 90.89 % Rotamer: Outliers : 0.52 % Allowed : 35.01 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.20), residues: 1712 helix: -5.40 (0.20), residues: 12 sheet: 0.30 (0.20), residues: 769 loop : -1.81 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 138 TYR 0.015 0.001 TYR H 146 PHE 0.008 0.001 PHE G 43 TRP 0.005 0.001 TRP G 38 HIS 0.002 0.001 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00315 (13161) covalent geometry : angle 0.77672 (17909) SS BOND : bond 0.00483 ( 16) SS BOND : angle 0.66859 ( 32) hydrogen bonds : bond 0.32196 ( 370) hydrogen bonds : angle 10.55379 ( 1014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASP cc_start: 0.8912 (m-30) cc_final: 0.8425 (t0) REVERT: H 25 MET cc_start: 0.7904 (ttm) cc_final: 0.7676 (tmm) outliers start: 7 outliers final: 1 residues processed: 122 average time/residue: 0.0997 time to fit residues: 18.3960 Evaluate side-chains 95 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 195 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 124 HIS ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN H 197 ASN ** I 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.039320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.028827 restraints weight = 150042.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.029589 restraints weight = 86525.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.030079 restraints weight = 62436.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.030404 restraints weight = 51090.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.030572 restraints weight = 44919.994| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 13177 Z= 0.274 Angle : 0.784 10.049 17941 Z= 0.407 Chirality : 0.047 0.256 2065 Planarity : 0.006 0.104 2311 Dihedral : 5.881 56.967 1839 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.05 % Favored : 90.65 % Rotamer: Outliers : 6.20 % Allowed : 28.88 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.20), residues: 1712 helix: -4.13 (0.76), residues: 18 sheet: 0.07 (0.19), residues: 768 loop : -1.72 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 54 TYR 0.019 0.002 TYR B 54 PHE 0.020 0.002 PHE B 137 TRP 0.013 0.002 TRP B 168 HIS 0.006 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00600 (13161) covalent geometry : angle 0.78219 (17909) SS BOND : bond 0.00871 ( 16) SS BOND : angle 1.32941 ( 32) hydrogen bonds : bond 0.04501 ( 370) hydrogen bonds : angle 7.23592 ( 1014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 91 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASP cc_start: 0.9249 (m-30) cc_final: 0.8631 (t70) REVERT: B 147 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7451 (pm20) REVERT: D 213 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7654 (m-10) REVERT: E 34 MET cc_start: 0.9237 (mmt) cc_final: 0.9022 (mmm) REVERT: E 73 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8776 (pptt) REVERT: H 77 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.7980 (tt) REVERT: H 180 LEU cc_start: 0.9104 (tp) cc_final: 0.8781 (pt) REVERT: I 176 ILE cc_start: 0.9673 (OUTLIER) cc_final: 0.9415 (mm) outliers start: 84 outliers final: 39 residues processed: 169 average time/residue: 0.0851 time to fit residues: 22.4226 Evaluate side-chains 130 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 86 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 210 CYS Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain H residue 8 HIS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 219 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 125 optimal weight: 0.0170 chunk 9 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS E 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.040141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.029524 restraints weight = 145268.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.030321 restraints weight = 83564.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.030833 restraints weight = 60209.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.031143 restraints weight = 48926.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.031230 restraints weight = 43205.121| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13177 Z= 0.127 Angle : 0.663 9.277 17941 Z= 0.341 Chirality : 0.046 0.199 2065 Planarity : 0.005 0.102 2311 Dihedral : 5.531 55.985 1839 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.18 % Favored : 91.53 % Rotamer: Outliers : 4.65 % Allowed : 29.32 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.20), residues: 1712 helix: -3.75 (0.89), residues: 18 sheet: 0.22 (0.19), residues: 769 loop : -1.68 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 54 TYR 0.017 0.001 TYR A 146 PHE 0.014 0.001 PHE A 109 TRP 0.008 0.001 TRP B 168 HIS 0.005 0.001 HIS I 167 Details of bonding type rmsd covalent geometry : bond 0.00285 (13161) covalent geometry : angle 0.66328 (17909) SS BOND : bond 0.00511 ( 16) SS BOND : angle 0.71887 ( 32) hydrogen bonds : bond 0.03612 ( 370) hydrogen bonds : angle 6.35453 ( 1014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 89 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASP cc_start: 0.9287 (m-30) cc_final: 0.8710 (t70) REVERT: C 34 MET cc_start: 0.8464 (mmm) cc_final: 0.8031 (tpt) REVERT: C 190 SER cc_start: 0.9569 (OUTLIER) cc_final: 0.9327 (p) REVERT: D 213 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7400 (m-10) REVERT: E 73 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8759 (pptt) REVERT: G 96 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8191 (ptm160) REVERT: G 180 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8374 (tp) REVERT: H 180 LEU cc_start: 0.9077 (tp) cc_final: 0.8792 (pt) REVERT: I 176 ILE cc_start: 0.9658 (OUTLIER) cc_final: 0.9429 (mm) outliers start: 63 outliers final: 37 residues processed: 147 average time/residue: 0.0992 time to fit residues: 22.1032 Evaluate side-chains 130 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 180 ILE Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 8 HIS Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 24 optimal weight: 0.0470 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.0040 chunk 106 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 HIS ** I 214 HIS ** 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 = 0.3269 r_free = 0.3269 target = 0.039190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.028611 restraints weight = 147123.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.029368 restraints weight = 84945.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.029845 restraints weight = 61307.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.030153 restraints weight = 50273.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.030339 restraints weight = 44369.185| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13177 Z= 0.206 Angle : 0.697 9.379 17941 Z= 0.356 Chirality : 0.046 0.177 2065 Planarity : 0.005 0.104 2311 Dihedral : 5.620 56.628 1839 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.94 % Favored : 90.83 % Rotamer: Outliers : 5.83 % Allowed : 28.73 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.20), residues: 1712 helix: -3.75 (0.89), residues: 18 sheet: 0.01 (0.19), residues: 772 loop : -1.68 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 134 TYR 0.018 0.002 TYR H 50 PHE 0.019 0.002 PHE B 137 TRP 0.010 0.001 TRP B 168 HIS 0.005 0.001 HIS I 167 Details of bonding type rmsd covalent geometry : bond 0.00456 (13161) covalent geometry : angle 0.69679 (17909) SS BOND : bond 0.00558 ( 16) SS BOND : angle 0.93339 ( 32) hydrogen bonds : bond 0.03480 ( 370) hydrogen bonds : angle 6.11884 ( 1014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 85 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8555 (mmt) cc_final: 0.8294 (mmp) REVERT: A 164 ASP cc_start: 0.9302 (m-30) cc_final: 0.8728 (t70) REVERT: B 135 THR cc_start: 0.6192 (OUTLIER) cc_final: 0.5971 (p) REVERT: B 202 GLU cc_start: 0.9361 (tm-30) cc_final: 0.9026 (pm20) REVERT: C 190 SER cc_start: 0.9552 (OUTLIER) cc_final: 0.9344 (p) REVERT: D 64 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: D 213 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7382 (m-10) REVERT: D 214 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7176 (mmm160) REVERT: E 73 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8805 (pptt) REVERT: H 77 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8357 (tt) REVERT: H 180 LEU cc_start: 0.9082 (tp) cc_final: 0.8792 (pt) REVERT: I 176 ILE cc_start: 0.9667 (OUTLIER) cc_final: 0.9425 (mm) outliers start: 79 outliers final: 50 residues processed: 157 average time/residue: 0.0866 time to fit residues: 21.2239 Evaluate side-chains 142 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 84 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 64 TYR Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 8 HIS Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 222 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 117 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** E 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.039037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.028484 restraints weight = 149390.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.029254 restraints weight = 85502.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.029734 restraints weight = 61369.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.030027 restraints weight = 50203.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.030229 restraints weight = 44443.840| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13177 Z= 0.195 Angle : 0.683 9.319 17941 Z= 0.349 Chirality : 0.045 0.164 2065 Planarity : 0.005 0.105 2311 Dihedral : 5.595 56.035 1839 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.76 % Favored : 91.00 % Rotamer: Outliers : 6.06 % Allowed : 28.80 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.20), residues: 1712 helix: -3.73 (0.87), residues: 18 sheet: -0.04 (0.19), residues: 767 loop : -1.67 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 44 TYR 0.016 0.002 TYR H 50 PHE 0.017 0.001 PHE B 137 TRP 0.012 0.001 TRP I 168 HIS 0.004 0.001 HIS I 167 Details of bonding type rmsd covalent geometry : bond 0.00436 (13161) covalent geometry : angle 0.68257 (17909) SS BOND : bond 0.00560 ( 16) SS BOND : angle 0.89665 ( 32) hydrogen bonds : bond 0.03410 ( 370) hydrogen bonds : angle 5.97814 ( 1014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 84 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8664 (mmt) cc_final: 0.8420 (mmp) REVERT: A 164 ASP cc_start: 0.9265 (m-30) cc_final: 0.8676 (t70) REVERT: B 135 THR cc_start: 0.6390 (OUTLIER) cc_final: 0.6159 (p) REVERT: B 192 MET cc_start: 0.9295 (mmm) cc_final: 0.8907 (mmm) REVERT: B 202 GLU cc_start: 0.9354 (tm-30) cc_final: 0.8992 (pm20) REVERT: C 79 LYS cc_start: 0.9718 (OUTLIER) cc_final: 0.9494 (mtmm) REVERT: C 190 SER cc_start: 0.9547 (OUTLIER) cc_final: 0.9340 (p) REVERT: D 213 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7311 (m-10) REVERT: D 214 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7220 (mmm160) REVERT: E 73 LYS cc_start: 0.9170 (pptt) cc_final: 0.8845 (pptt) REVERT: H 77 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8389 (tt) REVERT: H 180 LEU cc_start: 0.9088 (tp) cc_final: 0.8807 (pt) REVERT: I 176 ILE cc_start: 0.9681 (OUTLIER) cc_final: 0.9438 (mm) outliers start: 82 outliers final: 55 residues processed: 158 average time/residue: 0.0877 time to fit residues: 21.4114 Evaluate side-chains 146 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 84 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 150 TRP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 8 HIS Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 222 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 38 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 HIS ** 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 = 0.3259 r_free = 0.3259 target = 0.038893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.028358 restraints weight = 146688.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.029112 restraints weight = 84175.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.029599 restraints weight = 60679.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.029888 restraints weight = 49862.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.030069 restraints weight = 44056.919| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13177 Z= 0.178 Angle : 0.675 9.050 17941 Z= 0.344 Chirality : 0.045 0.157 2065 Planarity : 0.005 0.104 2311 Dihedral : 5.570 55.590 1839 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.05 % Favored : 90.77 % Rotamer: Outliers : 6.72 % Allowed : 28.43 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.20), residues: 1712 helix: -3.66 (0.88), residues: 18 sheet: -0.05 (0.19), residues: 768 loop : -1.62 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 44 TYR 0.015 0.001 TYR H 50 PHE 0.017 0.001 PHE A 109 TRP 0.008 0.001 TRP B 168 HIS 0.003 0.001 HIS I 167 Details of bonding type rmsd covalent geometry : bond 0.00400 (13161) covalent geometry : angle 0.67428 (17909) SS BOND : bond 0.00506 ( 16) SS BOND : angle 0.83518 ( 32) hydrogen bonds : bond 0.03214 ( 370) hydrogen bonds : angle 5.80333 ( 1014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 84 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8859 (mmt) cc_final: 0.8629 (mmp) REVERT: A 141 LEU cc_start: 0.9528 (pt) cc_final: 0.9045 (tp) REVERT: A 164 ASP cc_start: 0.9274 (m-30) cc_final: 0.8716 (t70) REVERT: B 135 THR cc_start: 0.6479 (OUTLIER) cc_final: 0.6222 (p) REVERT: B 192 MET cc_start: 0.9329 (mmm) cc_final: 0.9002 (mmm) REVERT: B 202 GLU cc_start: 0.9341 (tm-30) cc_final: 0.8981 (pm20) REVERT: C 79 LYS cc_start: 0.9713 (OUTLIER) cc_final: 0.9504 (mtmm) REVERT: D 213 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7250 (m-10) REVERT: D 214 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7224 (mmm160) REVERT: E 73 LYS cc_start: 0.9220 (pptt) cc_final: 0.8921 (pptt) REVERT: G 96 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8255 (ptm160) REVERT: H 77 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8385 (tt) REVERT: H 180 LEU cc_start: 0.9090 (tp) cc_final: 0.8823 (pt) REVERT: I 158 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8264 (tptp) REVERT: I 176 ILE cc_start: 0.9675 (OUTLIER) cc_final: 0.9395 (mm) outliers start: 91 outliers final: 68 residues processed: 168 average time/residue: 0.0767 time to fit residues: 19.8141 Evaluate side-chains 161 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 85 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 150 TRP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 8 HIS Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 222 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 25 optimal weight: 0.5980 chunk 132 optimal weight: 0.0870 chunk 107 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS G 42 GLN ** I 214 HIS ** 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 = 0.3265 r_free = 0.3265 target = 0.039024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028525 restraints weight = 146608.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.029274 restraints weight = 83674.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.029721 restraints weight = 60358.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.030048 restraints weight = 49487.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.030234 restraints weight = 43674.764| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13177 Z= 0.154 Angle : 0.677 13.025 17941 Z= 0.341 Chirality : 0.045 0.156 2065 Planarity : 0.005 0.105 2311 Dihedral : 5.491 55.338 1839 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.94 % Favored : 90.95 % Rotamer: Outliers : 6.72 % Allowed : 28.80 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.20), residues: 1712 helix: -3.61 (0.88), residues: 18 sheet: -0.01 (0.19), residues: 765 loop : -1.62 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 65 TYR 0.014 0.001 TYR H 50 PHE 0.023 0.001 PHE A 109 TRP 0.008 0.001 TRP B 168 HIS 0.012 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00349 (13161) covalent geometry : angle 0.67647 (17909) SS BOND : bond 0.00490 ( 16) SS BOND : angle 0.76259 ( 32) hydrogen bonds : bond 0.03099 ( 370) hydrogen bonds : angle 5.70524 ( 1014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 84 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8841 (mmt) cc_final: 0.8625 (mmp) REVERT: A 141 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9055 (tp) REVERT: A 164 ASP cc_start: 0.9274 (m-30) cc_final: 0.8717 (t70) REVERT: B 135 THR cc_start: 0.6436 (OUTLIER) cc_final: 0.6184 (p) REVERT: B 192 MET cc_start: 0.9406 (mmm) cc_final: 0.9149 (mmm) REVERT: C 79 LYS cc_start: 0.9703 (OUTLIER) cc_final: 0.9502 (mtmm) REVERT: D 213 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7254 (m-10) REVERT: D 214 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7225 (mmm160) REVERT: E 34 MET cc_start: 0.8998 (tpp) cc_final: 0.8572 (tpp) REVERT: E 73 LYS cc_start: 0.9217 (pptt) cc_final: 0.8921 (pptt) REVERT: G 96 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8131 (ptm160) REVERT: G 109 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8640 (mm) REVERT: G 128 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6793 (t-170) REVERT: H 77 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8387 (tt) REVERT: H 180 LEU cc_start: 0.9091 (tp) cc_final: 0.8826 (pt) REVERT: I 158 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8270 (tptp) REVERT: I 176 ILE cc_start: 0.9678 (OUTLIER) cc_final: 0.9362 (mm) outliers start: 91 outliers final: 67 residues processed: 167 average time/residue: 0.0889 time to fit residues: 22.8507 Evaluate side-chains 160 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 82 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 HIS Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 8 HIS Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 222 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN H 195 HIS ** I 214 HIS ** 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 = 0.3235 r_free = 0.3235 target = 0.038206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.027807 restraints weight = 149200.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.028512 restraints weight = 88406.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.028956 restraints weight = 64802.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.029236 restraints weight = 53620.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.029371 restraints weight = 47790.945| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 13177 Z= 0.296 Angle : 0.782 11.347 17941 Z= 0.398 Chirality : 0.046 0.161 2065 Planarity : 0.006 0.104 2311 Dihedral : 5.921 56.033 1839 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.57 % Favored : 89.31 % Rotamer: Outliers : 7.31 % Allowed : 28.58 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.20), residues: 1712 helix: -3.88 (0.83), residues: 20 sheet: -0.32 (0.19), residues: 762 loop : -1.73 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 44 TYR 0.019 0.002 TYR B 191 PHE 0.030 0.002 PHE A 109 TRP 0.011 0.002 TRP D 150 HIS 0.019 0.002 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00651 (13161) covalent geometry : angle 0.78131 (17909) SS BOND : bond 0.00635 ( 16) SS BOND : angle 1.14783 ( 32) hydrogen bonds : bond 0.03784 ( 370) hydrogen bonds : angle 6.08558 ( 1014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 75 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8861 (mmt) cc_final: 0.8615 (mmp) REVERT: B 135 THR cc_start: 0.6603 (OUTLIER) cc_final: 0.6390 (p) REVERT: B 192 MET cc_start: 0.9436 (mmm) cc_final: 0.9224 (mmm) REVERT: C 79 LYS cc_start: 0.9709 (OUTLIER) cc_final: 0.9487 (mtmm) REVERT: D 213 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7369 (m-10) REVERT: D 214 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6815 (mmm160) REVERT: E 73 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8934 (pptt) REVERT: G 96 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8241 (ptm160) REVERT: G 128 HIS cc_start: 0.7129 (OUTLIER) cc_final: 0.6899 (t-170) REVERT: H 77 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8447 (tt) REVERT: H 180 LEU cc_start: 0.9083 (tp) cc_final: 0.8819 (pt) REVERT: I 158 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8400 (tptp) REVERT: I 176 ILE cc_start: 0.9696 (OUTLIER) cc_final: 0.9328 (mm) outliers start: 99 outliers final: 74 residues processed: 165 average time/residue: 0.0897 time to fit residues: 22.2923 Evaluate side-chains 158 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 74 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 150 TRP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 64 TYR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 HIS Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 8 HIS Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 222 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 53 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 119 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS ** I 214 HIS ** 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 = 0.3262 r_free = 0.3262 target = 0.038940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.028418 restraints weight = 147774.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.029186 restraints weight = 83882.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.029676 restraints weight = 60303.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.029978 restraints weight = 49119.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.030158 restraints weight = 43414.143| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13177 Z= 0.138 Angle : 0.690 11.901 17941 Z= 0.348 Chirality : 0.046 0.152 2065 Planarity : 0.005 0.105 2311 Dihedral : 5.612 55.066 1839 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.94 % Favored : 90.95 % Rotamer: Outliers : 5.39 % Allowed : 30.35 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.20), residues: 1712 helix: -3.63 (0.89), residues: 18 sheet: -0.13 (0.19), residues: 766 loop : -1.68 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 59 TYR 0.016 0.001 TYR D 64 PHE 0.022 0.001 PHE A 109 TRP 0.011 0.001 TRP B 168 HIS 0.005 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00316 (13161) covalent geometry : angle 0.68989 (17909) SS BOND : bond 0.00454 ( 16) SS BOND : angle 0.65001 ( 32) hydrogen bonds : bond 0.03140 ( 370) hydrogen bonds : angle 5.69923 ( 1014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 82 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9512 (pt) cc_final: 0.9029 (tp) REVERT: B 135 THR cc_start: 0.6462 (OUTLIER) cc_final: 0.6203 (p) REVERT: B 192 MET cc_start: 0.9421 (mmm) cc_final: 0.9196 (mmm) REVERT: D 213 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7166 (m-10) REVERT: D 214 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7220 (mmm160) REVERT: E 34 MET cc_start: 0.9056 (tpp) cc_final: 0.8604 (mmm) REVERT: E 73 LYS cc_start: 0.9265 (pptt) cc_final: 0.8933 (pptt) REVERT: G 96 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8235 (ptm160) REVERT: G 128 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6634 (t-170) REVERT: H 77 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8411 (tt) REVERT: H 180 LEU cc_start: 0.9081 (tp) cc_final: 0.8837 (pt) REVERT: I 176 ILE cc_start: 0.9678 (OUTLIER) cc_final: 0.9339 (mm) outliers start: 73 outliers final: 59 residues processed: 147 average time/residue: 0.0809 time to fit residues: 18.1924 Evaluate side-chains 146 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 80 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 64 TYR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 191 CYS Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 128 HIS Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 HIS Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 222 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 90 optimal weight: 0.2980 chunk 129 optimal weight: 0.4980 chunk 106 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 72 optimal weight: 8.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN E 128 HIS ** I 214 HIS ** 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 = 0.3280 r_free = 0.3280 target = 0.039426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.028918 restraints weight = 144916.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029685 restraints weight = 82567.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.030190 restraints weight = 59266.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.030467 restraints weight = 48158.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.030672 restraints weight = 42795.126| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 13177 Z= 0.117 Angle : 0.702 12.019 17941 Z= 0.352 Chirality : 0.047 0.153 2065 Planarity : 0.005 0.105 2311 Dihedral : 5.426 54.632 1839 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.47 % Favored : 91.41 % Rotamer: Outliers : 4.58 % Allowed : 31.09 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.20), residues: 1712 helix: -3.55 (0.90), residues: 18 sheet: 0.06 (0.19), residues: 756 loop : -1.64 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 126 TYR 0.017 0.001 TYR D 143 PHE 0.015 0.001 PHE A 109 TRP 0.010 0.001 TRP B 168 HIS 0.017 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00272 (13161) covalent geometry : angle 0.70237 (17909) SS BOND : bond 0.00370 ( 16) SS BOND : angle 0.51446 ( 32) hydrogen bonds : bond 0.02920 ( 370) hydrogen bonds : angle 5.44510 ( 1014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 85 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9511 (pt) cc_final: 0.9024 (tp) REVERT: B 135 THR cc_start: 0.6461 (OUTLIER) cc_final: 0.6205 (p) REVERT: B 192 MET cc_start: 0.9415 (mmm) cc_final: 0.9192 (mmm) REVERT: C 34 MET cc_start: 0.8573 (mmm) cc_final: 0.7258 (mmm) REVERT: D 213 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7145 (m-10) REVERT: D 214 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7127 (mmm160) REVERT: E 73 LYS cc_start: 0.9249 (pptt) cc_final: 0.8936 (pptt) REVERT: G 96 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8171 (ptm160) REVERT: G 128 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.6526 (t-170) REVERT: H 25 MET cc_start: 0.8495 (ttm) cc_final: 0.7453 (tmm) REVERT: H 180 LEU cc_start: 0.9078 (tp) cc_final: 0.8853 (pt) REVERT: I 176 ILE cc_start: 0.9686 (OUTLIER) cc_final: 0.9382 (mm) REVERT: I 192 MET cc_start: 0.8890 (ptt) cc_final: 0.8485 (ptt) outliers start: 62 outliers final: 46 residues processed: 141 average time/residue: 0.0841 time to fit residues: 18.3779 Evaluate side-chains 135 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 83 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 64 TYR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 213 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 HIS Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 HIS Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 222 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.5743 > 50: distance: 61 - 115: 14.215 distance: 64 - 112: 5.520 distance: 71 - 103: 13.289 distance: 74 - 100: 16.697 distance: 89 - 91: 28.289 distance: 91 - 92: 28.598 distance: 92 - 93: 24.185 distance: 92 - 95: 33.620 distance: 93 - 94: 44.328 distance: 93 - 96: 21.504 distance: 96 - 97: 38.555 distance: 97 - 98: 24.065 distance: 98 - 99: 36.209 distance: 98 - 100: 18.857 distance: 100 - 101: 7.677 distance: 101 - 102: 13.857 distance: 101 - 104: 17.517 distance: 102 - 103: 19.074 distance: 102 - 107: 12.709 distance: 104 - 105: 4.442 distance: 104 - 106: 13.080 distance: 107 - 108: 10.076 distance: 108 - 109: 11.316 distance: 108 - 111: 23.215 distance: 109 - 110: 27.155 distance: 109 - 112: 17.988 distance: 112 - 113: 4.183 distance: 113 - 114: 5.424 distance: 113 - 116: 10.152 distance: 114 - 115: 6.006 distance: 114 - 119: 3.337 distance: 116 - 117: 21.692 distance: 116 - 118: 16.100 distance: 119 - 120: 5.748 distance: 120 - 121: 5.023 distance: 120 - 123: 12.170 distance: 121 - 122: 6.457 distance: 121 - 126: 7.905 distance: 123 - 124: 14.121 distance: 123 - 125: 21.614 distance: 126 - 127: 17.865 distance: 127 - 128: 48.108 distance: 127 - 130: 21.894 distance: 128 - 129: 12.748 distance: 128 - 133: 28.794 distance: 130 - 131: 26.525 distance: 130 - 132: 11.513 distance: 133 - 134: 4.745 distance: 134 - 135: 41.995 distance: 134 - 137: 62.574 distance: 135 - 136: 50.291 distance: 135 - 138: 33.093 distance: 138 - 139: 21.355 distance: 138 - 144: 25.125 distance: 139 - 140: 32.458 distance: 139 - 142: 40.330 distance: 140 - 141: 16.109 distance: 140 - 145: 15.191 distance: 142 - 143: 30.776 distance: 143 - 144: 15.988 distance: 145 - 146: 9.975 distance: 146 - 147: 8.278 distance: 146 - 149: 5.573 distance: 147 - 150: 8.078