Starting phenix.real_space_refine on Wed Jun 11 14:40:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5m_61146/06_2025/9j5m_61146.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5m_61146/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j5m_61146/06_2025/9j5m_61146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5m_61146/06_2025/9j5m_61146.map" model { file = "/net/cci-nas-00/data/ceres_data/9j5m_61146/06_2025/9j5m_61146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5m_61146/06_2025/9j5m_61146.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ARG:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 11, 'HIS: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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} 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: {'GLU:plan': 4, 'ARG:plan': 2, '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: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, '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: {'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6} 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: 8.47, per 1000 atoms: 0.66 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: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 2.10 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: 3.63 Time building geometry restraints manager: 3.40 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: 3.540 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.250 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- 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 : 12.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP G 38 HIS 0.002 0.001 HIS G 128 PHE 0.008 0.001 PHE G 43 TYR 0.015 0.001 TYR H 146 ARG 0.008 0.001 ARG C 138 Details of bonding type rmsd hydrogen bonds : bond 0.32196 ( 370) hydrogen bonds : angle 10.55379 ( 1014) SS BOND : bond 0.00483 ( 16) SS BOND : angle 0.66859 ( 32) covalent geometry : bond 0.00315 (13161) covalent geometry : angle 0.77672 (17909) *********************** 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 : 1.432 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: 0.2368 time to fit residues: 43.1631 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 : 1.530 ------------------------------------------------------------------------------- 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 142 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 43 optimal weight: 0.0010 chunk 86 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 H 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.040718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.029973 restraints weight = 144104.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.030751 restraints weight = 82572.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.031251 restraints weight = 59652.951| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13177 Z= 0.152 Angle : 0.708 9.141 17941 Z= 0.368 Chirality : 0.047 0.246 2065 Planarity : 0.006 0.103 2311 Dihedral : 5.550 55.798 1839 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.24 % Favored : 91.47 % Rotamer: Outliers : 4.36 % Allowed : 29.76 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.20), residues: 1712 helix: -4.13 (0.72), residues: 18 sheet: 0.27 (0.19), residues: 760 loop : -1.71 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 168 HIS 0.005 0.001 HIS I 167 PHE 0.013 0.001 PHE A 109 TYR 0.023 0.001 TYR A 146 ARG 0.006 0.001 ARG G 54 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 370) hydrogen bonds : angle 7.09280 ( 1014) SS BOND : bond 0.00611 ( 16) SS BOND : angle 1.03823 ( 32) covalent geometry : bond 0.00332 (13161) covalent geometry : angle 0.70704 (17909) *********************** 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 154 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 95 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASP cc_start: 0.9303 (m-30) cc_final: 0.8718 (t70) REVERT: B 147 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7772 (pm20) REVERT: C 34 MET cc_start: 0.8400 (tpt) cc_final: 0.8125 (tpt) REVERT: D 213 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7724 (m-10) REVERT: E 73 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8834 (pptt) REVERT: E 174 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7774 (mpp) REVERT: H 77 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.7917 (tt) REVERT: H 180 LEU cc_start: 0.9147 (tp) cc_final: 0.8795 (pt) REVERT: I 176 ILE cc_start: 0.9685 (OUTLIER) cc_final: 0.9485 (mm) outliers start: 59 outliers final: 21 residues processed: 148 average time/residue: 0.2189 time to fit residues: 49.0847 Evaluate side-chains 117 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 168 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 58 VAL 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 134 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 174 MET Chi-restraints excluded: chain H residue 8 HIS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 195 HIS Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 176 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 H 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.040073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.029425 restraints weight = 144552.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.030176 restraints weight = 84422.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.030659 restraints weight = 61263.949| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13177 Z= 0.150 Angle : 0.657 9.371 17941 Z= 0.338 Chirality : 0.045 0.193 2065 Planarity : 0.005 0.105 2311 Dihedral : 5.458 56.326 1839 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.41 % Favored : 91.41 % Rotamer: Outliers : 4.43 % Allowed : 29.25 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1712 helix: -3.79 (0.86), residues: 18 sheet: 0.31 (0.19), residues: 759 loop : -1.68 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 168 HIS 0.005 0.001 HIS I 167 PHE 0.012 0.001 PHE A 109 TYR 0.018 0.001 TYR A 146 ARG 0.005 0.000 ARG G 54 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 370) hydrogen bonds : angle 6.29896 ( 1014) SS BOND : bond 0.00537 ( 16) SS BOND : angle 0.82130 ( 32) covalent geometry : bond 0.00337 (13161) covalent geometry : angle 0.65683 (17909) *********************** 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 150 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 90 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ASP cc_start: 0.9276 (m-30) cc_final: 0.8703 (t70) REVERT: B 147 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: D 213 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7594 (m-10) REVERT: E 34 MET cc_start: 0.9182 (mmt) cc_final: 0.8937 (mmm) REVERT: E 73 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8818 (pptt) REVERT: G 96 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8036 (ptm160) REVERT: H 25 MET cc_start: 0.8428 (ttm) cc_final: 0.7367 (tmm) REVERT: H 77 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8064 (tt) REVERT: H 180 LEU cc_start: 0.9127 (tp) cc_final: 0.8789 (pt) REVERT: I 176 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9479 (mm) outliers start: 60 outliers final: 35 residues processed: 145 average time/residue: 0.2123 time to fit residues: 47.5795 Evaluate side-chains 127 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 124 HIS Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 200 VAL 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 B residue 227 PHE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 134 HIS 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 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 129 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 72 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.0050 chunk 27 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 ASN E 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.040081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.029408 restraints weight = 143530.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.030167 restraints weight = 84476.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.030622 restraints weight = 61577.419| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2322 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= 0.130 Angle : 0.646 8.966 17941 Z= 0.328 Chirality : 0.045 0.171 2065 Planarity : 0.005 0.105 2311 Dihedral : 5.293 55.665 1837 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.53 % Favored : 91.36 % Rotamer: Outliers : 3.62 % Allowed : 30.50 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.20), residues: 1712 helix: -3.67 (0.89), residues: 18 sheet: 0.27 (0.19), residues: 771 loop : -1.64 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 168 HIS 0.012 0.001 HIS A 124 PHE 0.013 0.001 PHE A 109 TYR 0.014 0.001 TYR A 146 ARG 0.004 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.03135 ( 370) hydrogen bonds : angle 5.92506 ( 1014) SS BOND : bond 0.00478 ( 16) SS BOND : angle 0.72382 ( 32) covalent geometry : bond 0.00295 (13161) covalent geometry : angle 0.64614 (17909) *********************** 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 137 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 88 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8600 (mmt) cc_final: 0.8300 (mmp) REVERT: A 164 ASP cc_start: 0.9272 (m-30) cc_final: 0.8718 (t70) REVERT: B 192 MET cc_start: 0.9381 (mmm) cc_final: 0.9078 (mmm) REVERT: B 202 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9128 (pm20) REVERT: C 190 SER cc_start: 0.9679 (OUTLIER) cc_final: 0.9439 (p) REVERT: D 213 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7616 (m-10) REVERT: D 214 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7003 (mmm160) REVERT: E 34 MET cc_start: 0.9146 (mmt) cc_final: 0.8894 (mmm) REVERT: E 73 LYS cc_start: 0.9226 (pptt) cc_final: 0.8865 (pptt) REVERT: H 77 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8268 (tt) REVERT: H 180 LEU cc_start: 0.9144 (tp) cc_final: 0.8792 (pt) REVERT: I 176 ILE cc_start: 0.9734 (OUTLIER) cc_final: 0.9507 (mm) outliers start: 49 outliers final: 35 residues processed: 133 average time/residue: 0.2204 time to fit residues: 44.7375 Evaluate side-chains 127 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 124 HIS Chi-restraints excluded: chain A residue 153 ASN 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 159 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 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 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 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 134 ARG 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 129 VAL 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 176 ILE Chi-restraints excluded: chain I residue 197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 10 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** 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 = 0.3275 r_free = 0.3275 target = 0.039380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.028818 restraints weight = 145659.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.029571 restraints weight = 83938.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.030057 restraints weight = 60530.523| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13177 Z= 0.192 Angle : 0.673 9.132 17941 Z= 0.343 Chirality : 0.045 0.163 2065 Planarity : 0.005 0.105 2311 Dihedral : 5.419 55.987 1837 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.46 % Favored : 90.42 % Rotamer: Outliers : 5.47 % Allowed : 29.10 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1712 helix: -3.68 (0.90), residues: 18 sheet: 0.13 (0.19), residues: 767 loop : -1.70 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 150 HIS 0.006 0.001 HIS A 124 PHE 0.019 0.002 PHE A 109 TYR 0.015 0.002 TYR H 50 ARG 0.005 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 370) hydrogen bonds : angle 5.84717 ( 1014) SS BOND : bond 0.00569 ( 16) SS BOND : angle 0.89744 ( 32) covalent geometry : bond 0.00430 (13161) covalent geometry : angle 0.67250 (17909) *********************** 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 161 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 87 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8691 (mmt) cc_final: 0.8480 (mmp) REVERT: A 164 ASP cc_start: 0.9304 (m-30) cc_final: 0.8748 (t70) REVERT: B 135 THR cc_start: 0.6264 (OUTLIER) cc_final: 0.6043 (p) REVERT: B 202 GLU cc_start: 0.9358 (tm-30) cc_final: 0.9012 (pm20) REVERT: C 34 MET cc_start: 0.8669 (tpt) cc_final: 0.8415 (mmm) REVERT: C 190 SER cc_start: 0.9566 (OUTLIER) cc_final: 0.9354 (p) REVERT: D 213 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7456 (m-10) REVERT: D 214 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7177 (mmm160) REVERT: E 73 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8829 (pptt) REVERT: G 96 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7933 (ptm160) REVERT: G 109 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8580 (mm) REVERT: H 77 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8321 (tt) REVERT: H 180 LEU cc_start: 0.9094 (tp) cc_final: 0.8802 (pt) REVERT: I 176 ILE cc_start: 0.9694 (OUTLIER) cc_final: 0.9479 (mm) outliers start: 74 outliers final: 47 residues processed: 156 average time/residue: 0.2289 time to fit residues: 52.9583 Evaluate side-chains 143 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 87 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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 124 HIS 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 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 46 VAL Chi-restraints excluded: chain C residue 68 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 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 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 73 LYS Chi-restraints excluded: chain E residue 128 HIS 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 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 129 VAL 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 77 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 99 optimal weight: 0.0470 chunk 163 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 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 = 0.3270 r_free = 0.3270 target = 0.039190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.028644 restraints weight = 147491.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.029388 restraints weight = 84261.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.029892 restraints weight = 60578.374| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2936 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= 0.185 Angle : 0.671 9.123 17941 Z= 0.340 Chirality : 0.045 0.158 2065 Planarity : 0.005 0.105 2311 Dihedral : 5.429 55.872 1837 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.35 % Favored : 90.54 % Rotamer: Outliers : 5.61 % Allowed : 29.39 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1712 helix: -3.70 (0.88), residues: 18 sheet: 0.07 (0.19), residues: 772 loop : -1.65 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 168 HIS 0.011 0.001 HIS A 124 PHE 0.021 0.001 PHE A 109 TYR 0.019 0.001 TYR D 64 ARG 0.004 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 370) hydrogen bonds : angle 5.76880 ( 1014) SS BOND : bond 0.00535 ( 16) SS BOND : angle 0.84758 ( 32) covalent geometry : bond 0.00412 (13161) covalent geometry : angle 0.67024 (17909) *********************** 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 162 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 86 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ASP cc_start: 0.9306 (m-30) cc_final: 0.8747 (t70) REVERT: B 106 LEU cc_start: 0.8683 (tp) cc_final: 0.8282 (pp) REVERT: B 135 THR cc_start: 0.6348 (OUTLIER) cc_final: 0.6136 (p) REVERT: B 192 MET cc_start: 0.9304 (mmm) cc_final: 0.9011 (mmm) REVERT: B 202 GLU cc_start: 0.9362 (tm-30) cc_final: 0.9005 (pm20) REVERT: C 190 SER cc_start: 0.9534 (OUTLIER) cc_final: 0.9328 (p) REVERT: D 213 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7378 (m-10) REVERT: D 214 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7212 (mmm160) REVERT: E 73 LYS cc_start: 0.9210 (pptt) cc_final: 0.8901 (pptt) REVERT: H 77 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8332 (tt) REVERT: H 180 LEU cc_start: 0.9102 (tp) cc_final: 0.8820 (pt) REVERT: I 176 ILE cc_start: 0.9714 (OUTLIER) cc_final: 0.9429 (mm) outliers start: 76 outliers final: 56 residues processed: 156 average time/residue: 0.2163 time to fit residues: 52.1945 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 : 1.735 ------------------------------------------------------------------------------- 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 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 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 159 PHE Chi-restraints excluded: chain B residue 227 PHE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 68 THR 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 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 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 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 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 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 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 106 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 25 optimal weight: 0.9990 chunk 128 optimal weight: 0.0020 chunk 74 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 HIS ** 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 = 0.3283 r_free = 0.3283 target = 0.039525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.028997 restraints weight = 145443.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.029756 restraints weight = 83211.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.030260 restraints weight = 59874.536| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13177 Z= 0.133 Angle : 0.651 9.925 17941 Z= 0.329 Chirality : 0.045 0.158 2065 Planarity : 0.005 0.105 2311 Dihedral : 5.308 55.260 1837 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.82 % Favored : 91.06 % Rotamer: Outliers : 4.65 % Allowed : 30.65 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.20), residues: 1712 helix: -3.66 (0.88), residues: 18 sheet: 0.12 (0.19), residues: 777 loop : -1.60 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 150 HIS 0.003 0.001 HIS I 167 PHE 0.018 0.001 PHE A 109 TYR 0.015 0.001 TYR D 64 ARG 0.004 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 370) hydrogen bonds : angle 5.54866 ( 1014) SS BOND : bond 0.00470 ( 16) SS BOND : angle 0.69638 ( 32) covalent geometry : bond 0.00305 (13161) covalent geometry : angle 0.65046 (17909) *********************** 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 148 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 85 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9521 (pt) cc_final: 0.9044 (tp) REVERT: A 164 ASP cc_start: 0.9292 (m-30) cc_final: 0.8741 (t70) REVERT: B 135 THR cc_start: 0.6339 (OUTLIER) cc_final: 0.6086 (p) REVERT: B 192 MET cc_start: 0.9332 (mmm) cc_final: 0.9076 (mmm) REVERT: D 213 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7279 (m-10) REVERT: D 214 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7159 (mmm160) REVERT: E 73 LYS cc_start: 0.9189 (pptt) cc_final: 0.8876 (pptt) REVERT: G 96 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7890 (ptm160) REVERT: G 109 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8558 (mm) REVERT: H 180 LEU cc_start: 0.9102 (tp) cc_final: 0.8818 (pt) REVERT: I 176 ILE cc_start: 0.9704 (OUTLIER) cc_final: 0.9432 (mm) outliers start: 63 outliers final: 51 residues processed: 143 average time/residue: 0.2209 time to fit residues: 48.7550 Evaluate side-chains 141 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 84 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 124 HIS 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 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 135 THR Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 GLU 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 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 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 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 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 208 ILE Chi-restraints excluded: chain H residue 55 ILE 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 106 LEU Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 3 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** 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 = 0.3232 r_free = 0.3232 target = 0.038141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.028699 restraints weight = 151795.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.028659 restraints weight = 97917.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.028856 restraints weight = 95645.422| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 13177 Z= 0.353 Angle : 0.828 10.544 17941 Z= 0.420 Chirality : 0.047 0.174 2065 Planarity : 0.006 0.105 2311 Dihedral : 5.887 56.820 1837 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.69 % Favored : 89.14 % Rotamer: Outliers : 6.28 % Allowed : 29.62 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.20), residues: 1712 helix: -3.95 (0.83), residues: 20 sheet: -0.28 (0.19), residues: 761 loop : -1.72 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 150 HIS 0.028 0.003 HIS E 128 PHE 0.032 0.002 PHE A 109 TYR 0.019 0.002 TYR H 50 ARG 0.006 0.001 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 370) hydrogen bonds : angle 6.15162 ( 1014) SS BOND : bond 0.00717 ( 16) SS BOND : angle 1.30370 ( 32) covalent geometry : bond 0.00778 (13161) covalent geometry : angle 0.82663 (17909) *********************** 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 162 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 77 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8284 (mmt) cc_final: 0.8057 (mmt) REVERT: B 135 THR cc_start: 0.6885 (OUTLIER) cc_final: 0.6677 (p) REVERT: C 79 LYS cc_start: 0.9721 (OUTLIER) cc_final: 0.9479 (mtmm) REVERT: D 213 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7603 (m-10) REVERT: D 214 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6853 (mmm160) REVERT: E 73 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9086 (pptt) REVERT: E 189 MET cc_start: 0.9019 (tpp) cc_final: 0.8818 (tpp) REVERT: H 77 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.8794 (tt) REVERT: H 180 LEU cc_start: 0.9103 (tp) cc_final: 0.8795 (pt) REVERT: I 158 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8291 (tptp) REVERT: I 176 ILE cc_start: 0.9782 (OUTLIER) cc_final: 0.9406 (mm) REVERT: I 192 MET cc_start: 0.9132 (ptt) cc_final: 0.8882 (ptt) outliers start: 85 outliers final: 62 residues processed: 153 average time/residue: 0.2141 time to fit residues: 49.8985 Evaluate side-chains 146 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 76 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 124 HIS 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 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 117 THR Chi-restraints excluded: chain B residue 123 ASP 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 134 HIS 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 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 73 LYS 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 54 ARG Chi-restraints excluded: chain G residue 117 LEU 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 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 137 ASN 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 50 VAL Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 77 THR 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 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 113 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN E 128 HIS G 42 GLN ** 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 = 0.3263 r_free = 0.3263 target = 0.038958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028452 restraints weight = 147090.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.029193 restraints weight = 83442.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.029668 restraints weight = 60276.069| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3498 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= 0.152 Angle : 0.704 13.500 17941 Z= 0.353 Chirality : 0.046 0.155 2065 Planarity : 0.005 0.105 2311 Dihedral : 5.602 55.828 1837 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.59 % Favored : 91.30 % Rotamer: Outliers : 4.73 % Allowed : 31.46 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.20), residues: 1712 helix: -3.62 (0.89), residues: 18 sheet: -0.13 (0.19), residues: 768 loop : -1.64 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 150 HIS 0.005 0.001 HIS E 128 PHE 0.022 0.001 PHE A 109 TYR 0.016 0.001 TYR D 64 ARG 0.004 0.000 ARG G 134 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 370) hydrogen bonds : angle 5.76025 ( 1014) SS BOND : bond 0.00497 ( 16) SS BOND : angle 0.71771 ( 32) covalent geometry : bond 0.00343 (13161) covalent geometry : angle 0.70388 (17909) *********************** 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 146 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 82 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9521 (pt) cc_final: 0.9049 (tp) REVERT: A 159 LYS cc_start: 0.6146 (tppt) cc_final: 0.5714 (tppt) REVERT: B 135 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6337 (p) REVERT: D 213 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7317 (m-10) REVERT: D 214 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7211 (mmm160) REVERT: E 73 LYS cc_start: 0.9233 (pptt) cc_final: 0.8939 (pptt) REVERT: G 96 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8295 (ptm160) REVERT: G 128 HIS cc_start: 0.7043 (OUTLIER) cc_final: 0.6733 (t-90) REVERT: H 77 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8380 (tt) REVERT: H 180 LEU cc_start: 0.9078 (tp) cc_final: 0.8806 (pt) REVERT: I 176 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9344 (mm) REVERT: I 192 MET cc_start: 0.8973 (ptt) cc_final: 0.8649 (ptt) outliers start: 64 outliers final: 50 residues processed: 139 average time/residue: 0.2204 time to fit residues: 47.0306 Evaluate side-chains 136 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 79 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 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 48 PHE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 131 SER 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 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 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 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 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 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 106 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 30 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** E 128 HIS ** 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 = 0.3274 r_free = 0.3274 target = 0.039225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028737 restraints weight = 145003.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.029476 restraints weight = 82313.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.029943 restraints weight = 59444.174| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13177 Z= 0.131 Angle : 0.704 12.317 17941 Z= 0.351 Chirality : 0.046 0.155 2065 Planarity : 0.005 0.106 2311 Dihedral : 5.434 55.248 1837 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.88 % Favored : 91.00 % Rotamer: Outliers : 4.28 % Allowed : 32.13 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1712 helix: -3.55 (0.91), residues: 18 sheet: -0.00 (0.19), residues: 771 loop : -1.62 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 150 HIS 0.008 0.001 HIS E 128 PHE 0.019 0.001 PHE A 109 TYR 0.015 0.001 TYR D 143 ARG 0.008 0.000 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 370) hydrogen bonds : angle 5.55378 ( 1014) SS BOND : bond 0.00424 ( 16) SS BOND : angle 0.64481 ( 32) covalent geometry : bond 0.00306 (13161) covalent geometry : angle 0.70459 (17909) ********************** 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 142 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 84 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.9513 (pt) cc_final: 0.9026 (tp) REVERT: A 159 LYS cc_start: 0.6205 (tppt) cc_final: 0.5790 (tppt) REVERT: B 135 THR cc_start: 0.6618 (OUTLIER) cc_final: 0.6387 (p) REVERT: D 213 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7246 (m-10) REVERT: D 214 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7182 (mmm160) REVERT: E 73 LYS cc_start: 0.9261 (pptt) cc_final: 0.8972 (pptt) REVERT: E 166 MET cc_start: 0.8798 (pmm) cc_final: 0.8553 (ppp) REVERT: G 96 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8255 (ptm160) REVERT: G 128 HIS cc_start: 0.7010 (OUTLIER) cc_final: 0.6765 (t-170) REVERT: H 77 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8360 (tt) REVERT: H 180 LEU cc_start: 0.9085 (tp) cc_final: 0.8812 (pt) REVERT: I 176 ILE cc_start: 0.9710 (OUTLIER) cc_final: 0.9371 (mm) outliers start: 58 outliers final: 49 residues processed: 135 average time/residue: 0.2254 time to fit residues: 46.2414 Evaluate side-chains 138 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 82 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 124 HIS Chi-restraints excluded: chain A residue 153 ASN 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 105 GLU Chi-restraints excluded: chain B residue 131 SER 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 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 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 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 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 106 LEU Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 140 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 100 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 107 optimal weight: 0.0370 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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** H 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.039737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.029223 restraints weight = 143903.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.029980 restraints weight = 82020.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.030482 restraints weight = 59200.445| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13177 Z= 0.115 Angle : 0.695 12.370 17941 Z= 0.344 Chirality : 0.046 0.155 2065 Planarity : 0.005 0.106 2311 Dihedral : 5.255 55.134 1837 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.29 % Favored : 91.59 % Rotamer: Outliers : 3.99 % Allowed : 32.27 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.06 % Twisted Proline : 3.33 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1712 helix: -3.50 (0.92), residues: 18 sheet: 0.14 (0.19), residues: 759 loop : -1.61 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 150 HIS 0.003 0.001 HIS I 167 PHE 0.015 0.001 PHE A 109 TYR 0.016 0.001 TYR D 143 ARG 0.005 0.000 ARG G 134 Details of bonding type rmsd hydrogen bonds : bond 0.02686 ( 370) hydrogen bonds : angle 5.30132 ( 1014) SS BOND : bond 0.00374 ( 16) SS BOND : angle 0.50698 ( 32) covalent geometry : bond 0.00269 (13161) covalent geometry : angle 0.69565 (17909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4919.25 seconds wall clock time: 85 minutes 53.02 seconds (5153.02 seconds total)