Starting phenix.real_space_refine on Sun May 18 17:30:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e5g_47526/05_2025/9e5g_47526.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e5g_47526/05_2025/9e5g_47526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e5g_47526/05_2025/9e5g_47526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e5g_47526/05_2025/9e5g_47526.map" model { file = "/net/cci-nas-00/data/ceres_data/9e5g_47526/05_2025/9e5g_47526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e5g_47526/05_2025/9e5g_47526.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9279 atoms to isotropic. 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 42 5.16 5 C 6302 2.51 5 N 1730 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9927 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1625 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1619 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 220, 1619 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 1649 Chain: "B" Number of atoms: 1636 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 219, 1633 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Conformer: "B" Number of residues, atoms: 219, 1633 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 bond proxies already assigned to first conformer: 1665 Chain: "C" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1644 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1636 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 67 Chain: "E" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1641 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 7, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1652 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Unusual residues: {'ACT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 8.71, per 1000 atoms: 0.88 Number of scatterers: 9927 At special positions: 0 Unit cell: (97.148, 96.496, 84.108, 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 42 16.00 O 1853 8.00 N 1730 7.00 C 6302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.66 Conformation dependent library (CDL) restraints added in 1.9 seconds 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 14 sheets defined 50.8% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.550A pdb=" N ILE A 49 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 70 Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 138 through 149 removed outlier: 4.006A pdb=" N PHE A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 4.422A pdb=" N SER A 170 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.630A pdb=" N ILE B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 70 Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.985A pdb=" N PHE B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 4.610A pdb=" N SER B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'C' and resid 5 through 20 Processing helix chain 'C' and resid 45 through 50 removed outlier: 3.715A pdb=" N ILE C 49 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 70 Processing helix chain 'C' and resid 85 through 97 Processing helix chain 'C' and resid 138 through 149 removed outlier: 4.192A pdb=" N PHE C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 removed outlier: 4.604A pdb=" N SER C 170 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 175 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'D' and resid 5 through 20 Processing helix chain 'D' and resid 45 through 50 removed outlier: 3.593A pdb=" N ILE D 49 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 70 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.977A pdb=" N PHE D 142 " --> pdb=" O SER D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 4.604A pdb=" N SER D 170 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 196 Processing helix chain 'D' and resid 199 through 212 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'E' and resid 5 through 20 Processing helix chain 'E' and resid 45 through 50 removed outlier: 3.840A pdb=" N ILE E 49 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 70 Processing helix chain 'E' and resid 85 through 97 Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.928A pdb=" N PHE E 142 " --> pdb=" O SER E 138 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 removed outlier: 4.539A pdb=" N SER E 170 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE E 175 " --> pdb=" O VAL E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 196 Processing helix chain 'E' and resid 199 through 212 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 45 through 50 removed outlier: 3.674A pdb=" N ILE F 49 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 70 Processing helix chain 'F' and resid 85 through 97 Processing helix chain 'F' and resid 138 through 149 removed outlier: 4.004A pdb=" N PHE F 142 " --> pdb=" O SER F 138 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 185 through 196 Processing helix chain 'F' and resid 199 through 212 Processing helix chain 'F' and resid 212 through 220 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.636A pdb=" N TYR A 102 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL A 78 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 103 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 80 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA A 77 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL A 129 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA A 79 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ASP A 131 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 126 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE A 157 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU A 128 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU A 159 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N GLU A 130 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N HIS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N LEU A 132 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 179 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 157 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA A 181 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU A 159 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 183 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 117 removed outlier: 6.153A pdb=" N VAL B 78 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL B 103 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY B 80 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA B 77 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL B 129 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 79 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ASP B 131 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N GLY B 81 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 11.824A pdb=" N THR B 133 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 126 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N PHE B 157 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU B 128 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LEU B 159 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N GLU B 130 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N HIS B 161 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N LEU B 132 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N ASP B 178 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN B 154 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N HIS B 180 " --> pdb=" O ASN B 154 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYS B 156 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LEU B 182 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N VAL B 158 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR B 184 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE B 160 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AA7, first strand: chain 'C' and resid 116 through 117 removed outlier: 6.048A pdb=" N VAL C 78 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL C 103 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY C 80 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA C 77 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL C 129 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA C 79 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N ASP C 131 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C 126 " --> pdb=" O HIS C 155 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE C 157 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU C 128 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU C 159 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N GLU C 130 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N HIS C 161 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N LEU C 132 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N ASP C 178 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN C 154 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N HIS C 180 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N CYS C 156 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU C 182 " --> pdb=" O CYS C 156 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL C 158 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR C 184 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE C 160 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 23 through 25 Processing sheet with id=AA9, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.109A pdb=" N VAL D 78 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL D 103 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY D 80 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA D 77 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL D 129 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA D 79 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ASP D 131 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 126 " --> pdb=" O HIS D 155 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE D 157 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU D 128 " --> pdb=" O PHE D 157 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU D 159 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N GLU D 130 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N HIS D 161 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LEU D 132 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ASP D 178 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN D 154 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N HIS D 180 " --> pdb=" O ASN D 154 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N CYS D 156 " --> pdb=" O HIS D 180 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LEU D 182 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N VAL D 158 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR D 184 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N PHE D 160 " --> pdb=" O THR D 184 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 23 through 25 Processing sheet with id=AB2, first strand: chain 'E' and resid 116 through 117 removed outlier: 6.059A pdb=" N VAL E 78 " --> pdb=" O GLN E 101 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL E 103 " --> pdb=" O VAL E 78 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY E 80 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL E 126 " --> pdb=" O HIS E 155 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N PHE E 157 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU E 128 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU E 159 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N GLU E 130 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N HIS E 161 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N LEU E 132 " --> pdb=" O HIS E 161 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N ASP E 178 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN E 154 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N HIS E 180 " --> pdb=" O ASN E 154 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS E 156 " --> pdb=" O HIS E 180 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LEU E 182 " --> pdb=" O CYS E 156 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N VAL E 158 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N THR E 184 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N PHE E 160 " --> pdb=" O THR E 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 23 through 25 Processing sheet with id=AB4, first strand: chain 'F' and resid 31 through 32 Processing sheet with id=AB5, first strand: chain 'F' and resid 116 through 117 removed outlier: 6.041A pdb=" N VAL F 78 " --> pdb=" O GLN F 101 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL F 103 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY F 80 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP F 131 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F 126 " --> pdb=" O HIS F 155 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N PHE F 157 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU F 128 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU F 159 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N GLU F 130 " --> pdb=" O LEU F 159 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N HIS F 161 " --> pdb=" O GLU F 130 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N LEU F 132 " --> pdb=" O HIS F 161 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU F 182 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N PHE F 160 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR F 184 " --> pdb=" O PHE F 160 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1349 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 3.03 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: 3223 1.34 - 1.46: 1472 1.46 - 1.57: 5304 1.57 - 1.69: 1 1.69 - 1.81: 72 Bond restraints: 10072 Sorted by residual: bond pdb=" CA THR C 2 " pdb=" C THR C 2 " ideal model delta sigma weight residual 1.525 1.591 -0.066 2.10e-02 2.27e+03 1.00e+01 bond pdb=" CB SER E 136 " pdb=" OG SER E 136 " ideal model delta sigma weight residual 1.417 1.364 0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" CA SER E 136 " pdb=" C SER E 136 " ideal model delta sigma weight residual 1.526 1.498 0.027 1.39e-02 5.18e+03 3.87e+00 bond pdb=" CA SER E 136 " pdb=" CB SER E 136 " ideal model delta sigma weight residual 1.530 1.503 0.028 1.54e-02 4.22e+03 3.23e+00 bond pdb=" CA GLY C 3 " pdb=" C GLY C 3 " ideal model delta sigma weight residual 1.510 1.529 -0.019 1.18e-02 7.18e+03 2.61e+00 ... (remaining 10067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 13550 1.84 - 3.67: 158 3.67 - 5.51: 13 5.51 - 7.34: 4 7.34 - 9.18: 3 Bond angle restraints: 13728 Sorted by residual: angle pdb=" CA GLY C 3 " pdb=" C GLY C 3 " pdb=" N TYR C 4 " ideal model delta sigma weight residual 114.48 120.37 -5.89 1.19e+00 7.06e-01 2.45e+01 angle pdb=" C THR C 2 " pdb=" CA THR C 2 " pdb=" CB THR C 2 " ideal model delta sigma weight residual 109.10 118.23 -9.13 2.20e+00 2.07e-01 1.72e+01 angle pdb=" CA GLY C 3 " pdb=" C GLY C 3 " pdb=" O GLY C 3 " ideal model delta sigma weight residual 121.87 118.63 3.24 1.02e+00 9.61e-01 1.01e+01 angle pdb=" CB MET F 59 " pdb=" CG MET F 59 " pdb=" SD MET F 59 " ideal model delta sigma weight residual 112.70 121.88 -9.18 3.00e+00 1.11e-01 9.36e+00 angle pdb=" C GLY A 85 " pdb=" N ILE A 86 " pdb=" CA ILE A 86 " ideal model delta sigma weight residual 120.33 122.68 -2.35 8.00e-01 1.56e+00 8.64e+00 ... (remaining 13723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 5090 16.33 - 32.67: 563 32.67 - 49.00: 156 49.00 - 65.33: 40 65.33 - 81.66: 12 Dihedral angle restraints: 5861 sinusoidal: 2053 harmonic: 3808 Sorted by residual: dihedral pdb=" C THR C 2 " pdb=" N THR C 2 " pdb=" CA THR C 2 " pdb=" CB THR C 2 " ideal model delta harmonic sigma weight residual -122.00 -138.44 16.44 0 2.50e+00 1.60e-01 4.32e+01 dihedral pdb=" C SER E 136 " pdb=" N SER E 136 " pdb=" CA SER E 136 " pdb=" CB SER E 136 " ideal model delta harmonic sigma weight residual -122.60 -133.67 11.07 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" N THR C 2 " pdb=" C THR C 2 " pdb=" CA THR C 2 " pdb=" CB THR C 2 " ideal model delta harmonic sigma weight residual 123.40 134.26 -10.86 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 5858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1588 0.109 - 0.217: 17 0.217 - 0.326: 0 0.326 - 0.435: 0 0.435 - 0.543: 2 Chirality restraints: 1607 Sorted by residual: chirality pdb=" CA THR C 2 " pdb=" N THR C 2 " pdb=" C THR C 2 " pdb=" CB THR C 2 " both_signs ideal model delta sigma weight residual False 2.53 1.98 0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CA SER E 136 " pdb=" N SER E 136 " pdb=" C SER E 136 " pdb=" CB SER E 136 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.12e+00 chirality pdb=" CB VAL B 98 " pdb=" CA VAL B 98 " pdb=" CG1 VAL B 98 " pdb=" CG2 VAL B 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 1604 not shown) Planarity restraints: 1751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 98 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO B 99 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 83 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C THR B 83 " 0.026 2.00e-02 2.50e+03 pdb=" O THR B 83 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 84 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 98 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO C 99 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.020 5.00e-02 4.00e+02 ... (remaining 1748 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2107 2.78 - 3.31: 9068 3.31 - 3.84: 16965 3.84 - 4.37: 19674 4.37 - 4.90: 36161 Nonbonded interactions: 83975 Sorted by model distance: nonbonded pdb=" OG SER D 136 " pdb=" O SER D 168 " model vdw 2.253 3.040 nonbonded pdb=" OD1 ASP D 131 " pdb=" N LEU D 132 " model vdw 2.264 3.120 nonbonded pdb=" OD1 ASP C 11 " pdb=" NH1 ARG C 190 " model vdw 2.282 3.120 nonbonded pdb=" O GLY F 3 " pdb=" O HOH F 301 " model vdw 2.299 3.040 nonbonded pdb=" O THR B 83 " pdb=" OH TYR E 102 " model vdw 2.305 3.040 ... (remaining 83970 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 9 or resid 11 through 32 or (resid 35 and (name \ N or name CA or name C or name O or name CB )) or resid 36 through 46 or resid 4 \ 8 through 109 or resid 112 through 175 or (resid 176 and (name N or name CA or n \ ame C or name O or name CB )) or resid 177 through 219 or (resid 220 and (name N \ or name CA or name C or name O or name CB )) or resid 221 through 222)) selection = (chain 'B' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 9 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 25 or (resid 26 through 29 \ and (name N or name CA or name C or name O or name CB )) or resid 30 through 32 \ or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 46 or resid 48 through 109 or resid 112 through 116 or (resid 117 and \ (name N or name CA or name C or name O or name CB )) or resid 118 through 121 o \ r (resid 122 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 23 through 172 or (resid 173 through 174 and (name N or name CA or name C or nam \ e O or name CB )) or resid 175 through 199 or (resid 200 through 201 and (name N \ or name CA or name C or name O or name CB )) or resid 202 through 207 or (resid \ 208 and (name N or name CA or name C or name O or name CB )) or resid 209 throu \ gh 219 or (resid 220 and (name N or name CA or name C or name O or name CB )) or \ resid 221 through 222)) selection = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 9 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 25 or (resid 26 through 29 \ and (name N or name CA or name C or name O or name CB )) or resid 30 through 46 \ or resid 48 through 109 or resid 112 through 116 or (resid 117 and (name N or n \ ame CA or name C or name O or name CB )) or resid 118 through 121 or (resid 122 \ and (name N or name CA or name C or name O or name CB )) or resid 123 through 13 \ 6 or (resid 137 and (name N or name CA or name C or name O or name CB )) or resi \ d 138 through 172 or (resid 173 through 174 and (name N or name CA or name C or \ name O or name CB )) or resid 175 through 199 or (resid 200 through 201 and (nam \ e N or name CA or name C or name O or name CB )) or resid 202 through 203 or (re \ sid 204 through 205 and (name N or name CA or name C or name O or name CB )) or \ resid 206 through 207 or (resid 208 and (name N or name CA or name C or name O o \ r name CB )) or resid 209 through 219 or (resid 220 and (name N or name CA or na \ me C or name O or name CB )) or resid 221 through 222)) selection = (chain 'D' and (resid 2 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 9 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 25 or (resid 26 through 29 \ and (name N or name CA or name C or name O or name CB )) or resid 30 through 32 \ or (resid 35 and (name N or name CA or name C or name O or name CB )) or resid \ 36 through 46 or resid 48 through 104 or (resid 105 through 106 and (name N or n \ ame CA or name C or name O or name CB )) or resid 107 through 116 or (resid 117 \ and (name N or name CA or name C or name O or name CB )) or resid 118 through 17 \ 2 or (resid 173 through 174 and (name N or name CA or name C or name O or name C \ B )) or resid 175 through 199 or (resid 200 through 201 and (name N or name CA o \ r name C or name O or name CB )) or resid 202 through 203 or (resid 204 through \ 205 and (name N or name CA or name C or name O or name CB )) or resid 206 or (re \ sid 207 through 208 and (name N or name CA or name C or name O or name CB )) or \ resid 209 through 219 or (resid 220 and (name N or name CA or name C or name O o \ r name CB )) or resid 221 through 222)) selection = (chain 'E' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 9 or resid 11 through 25 or (resid 26 \ through 29 and (name N or name CA or name C or name O or name CB )) or resid 30 \ through 32 or (resid 35 and (name N or name CA or name C or name O or name CB )) \ or resid 36 through 46 or resid 48 through 109 or resid 112 through 116 or (res \ id 117 and (name N or name CA or name C or name O or name CB )) or resid 118 thr \ ough 172 or (resid 173 through 174 and (name N or name CA or name C or name O or \ name CB )) or resid 175 or (resid 176 and (name N or name CA or name C or name \ O or name CB )) or resid 177 through 199 or (resid 200 through 201 and (name N o \ r name CA or name C or name O or name CB )) or resid 202 through 203 or (resid 2 \ 04 through 205 and (name N or name CA or name C or name O or name CB )) or resid \ 206 through 219 or (resid 220 and (name N or name CA or name C or name O or nam \ e CB )) or resid 221 through 222)) selection = (chain 'F' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 9 or resid 11 through 25 or (resid 26 \ through 29 and (name N or name CA or name C or name O or name CB )) or resid 30 \ through 32 or (resid 35 and (name N or name CA or name C or name O or name CB )) \ or resid 36 through 46 or resid 48 through 104 or (resid 105 through 106 and (n \ ame N or name CA or name C or name O or name CB )) or resid 107 through 109 or r \ esid 112 through 116 or (resid 117 and (name N or name CA or name C or name O or \ name CB )) or resid 118 through 120 or (resid 121 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 136 or (resid 137 a \ nd (name N or name CA or name C or name O or name CB )) or resid 138 through 175 \ or (resid 176 and (name N or name CA or name C or name O or name CB )) or resid \ 177 through 204 or (resid 205 and (name N or name CA or name C or name O or nam \ e CB )) or resid 206 through 222)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.19 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.550 Find NCS groups from input model: 0.600 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 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 0.066 10072 Z= 0.144 Angle : 0.502 9.178 13728 Z= 0.279 Chirality : 0.044 0.543 1607 Planarity : 0.003 0.046 1751 Dihedral : 15.868 81.664 3387 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.40 % Favored : 97.45 % Rotamer: Outliers : 0.42 % Allowed : 20.00 % Favored : 79.58 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.23), residues: 1296 helix: 1.88 (0.21), residues: 607 sheet: 0.85 (0.37), residues: 185 loop : -0.79 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 216 HIS 0.002 0.001 HIS A 155 PHE 0.007 0.001 PHE C 157 TYR 0.014 0.001 TYR E 102 ARG 0.005 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.14814 ( 468) hydrogen bonds : angle 4.36251 ( 1349) covalent geometry : bond 0.00314 (10072) covalent geometry : angle 0.50152 (13728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7682 (mt0) cc_final: 0.7443 (tt0) REVERT: B 130 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6564 (tp30) REVERT: C 53 ARG cc_start: 0.6925 (mtm-85) cc_final: 0.5818 (mtp180) REVERT: E 47 LYS cc_start: 0.6329 (mtpt) cc_final: 0.5529 (mmtp) REVERT: F 76 ASP cc_start: 0.6815 (m-30) cc_final: 0.6437 (m-30) outliers start: 2 outliers final: 1 residues processed: 141 average time/residue: 0.2553 time to fit residues: 48.8065 Evaluate side-chains 105 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 ASN D 74 GLN E 180 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.151400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.134840 restraints weight = 12505.374| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 0.83 r_work: 0.3112 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 10072 Z= 0.134 Angle : 0.508 5.360 13728 Z= 0.272 Chirality : 0.042 0.182 1607 Planarity : 0.004 0.044 1751 Dihedral : 3.604 18.833 1403 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.01 % Favored : 96.83 % Rotamer: Outliers : 1.68 % Allowed : 17.59 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1296 helix: 1.55 (0.21), residues: 628 sheet: 0.96 (0.37), residues: 172 loop : -0.93 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 216 HIS 0.004 0.001 HIS A 155 PHE 0.010 0.001 PHE C 209 TYR 0.019 0.002 TYR F 102 ARG 0.006 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.02997 ( 468) hydrogen bonds : angle 3.67734 ( 1349) covalent geometry : bond 0.00317 (10072) covalent geometry : angle 0.50760 (13728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.071 Fit side-chains REVERT: A 21 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7223 (mt0) REVERT: D 173 LYS cc_start: 0.6959 (mmtp) cc_final: 0.6318 (tptp) REVERT: E 47 LYS cc_start: 0.8020 (mtpt) cc_final: 0.7443 (mmtm) REVERT: E 100 MET cc_start: 0.8775 (tmm) cc_final: 0.8470 (ttt) outliers start: 15 outliers final: 8 residues processed: 130 average time/residue: 0.1890 time to fit residues: 36.2876 Evaluate side-chains 119 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 2 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.146092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.130930 restraints weight = 19184.767| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.20 r_work: 0.2991 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 10072 Z= 0.128 Angle : 0.468 6.151 13728 Z= 0.252 Chirality : 0.042 0.348 1607 Planarity : 0.004 0.043 1751 Dihedral : 3.511 14.046 1402 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.17 % Favored : 96.68 % Rotamer: Outliers : 1.78 % Allowed : 17.91 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1296 helix: 1.82 (0.22), residues: 630 sheet: 0.78 (0.36), residues: 175 loop : -0.90 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 186 HIS 0.006 0.001 HIS F 24 PHE 0.011 0.001 PHE E 142 TYR 0.014 0.002 TYR F 102 ARG 0.008 0.001 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 468) hydrogen bonds : angle 3.42285 ( 1349) covalent geometry : bond 0.00314 (10072) covalent geometry : angle 0.46777 (13728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.042 Fit side-chains REVERT: A 21 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: A 115 GLN cc_start: 0.8778 (tt0) cc_final: 0.8209 (tt0) REVERT: A 130 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 193 LYS cc_start: 0.7893 (mtpp) cc_final: 0.7622 (mtmt) REVERT: B 15 LYS cc_start: 0.8269 (mtmm) cc_final: 0.7974 (mtmt) REVERT: C 15 LYS cc_start: 0.8418 (mtmm) cc_final: 0.8019 (mtmt) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.1961 time to fit residues: 37.5454 Evaluate side-chains 119 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 78 optimal weight: 0.0030 chunk 15 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.4948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.149639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.140427 restraints weight = 15093.109| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 0.75 r_work: 0.3179 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10072 Z= 0.092 Angle : 0.411 5.111 13728 Z= 0.223 Chirality : 0.040 0.157 1607 Planarity : 0.003 0.043 1751 Dihedral : 3.314 13.440 1402 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.22 % Rotamer: Outliers : 1.78 % Allowed : 17.17 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1296 helix: 1.90 (0.21), residues: 630 sheet: 0.79 (0.36), residues: 176 loop : -0.88 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 185 HIS 0.002 0.001 HIS A 155 PHE 0.006 0.001 PHE D 157 TYR 0.013 0.001 TYR B 102 ARG 0.003 0.000 ARG F 56 Details of bonding type rmsd hydrogen bonds : bond 0.02416 ( 468) hydrogen bonds : angle 3.29420 ( 1349) covalent geometry : bond 0.00208 (10072) covalent geometry : angle 0.41138 (13728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.135 Fit side-chains REVERT: A 21 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7345 (mt0) REVERT: A 130 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7857 (mm-30) REVERT: B 15 LYS cc_start: 0.8360 (mtmm) cc_final: 0.8121 (mtmt) REVERT: C 15 LYS cc_start: 0.8392 (mtmm) cc_final: 0.8079 (mtmt) REVERT: C 76 ASP cc_start: 0.8563 (m-30) cc_final: 0.8318 (m-30) REVERT: D 173 LYS cc_start: 0.7093 (mmtp) cc_final: 0.6600 (tptt) REVERT: E 47 LYS cc_start: 0.8572 (mtpt) cc_final: 0.8020 (mmtm) outliers start: 16 outliers final: 12 residues processed: 125 average time/residue: 0.1889 time to fit residues: 35.0771 Evaluate side-chains 120 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.140818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.114980 restraints weight = 18174.459| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.83 r_work: 0.2885 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10072 Z= 0.170 Angle : 0.509 6.092 13728 Z= 0.274 Chirality : 0.043 0.218 1607 Planarity : 0.004 0.046 1751 Dihedral : 3.874 16.418 1402 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.63 % Favored : 96.21 % Rotamer: Outliers : 2.93 % Allowed : 16.34 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1296 helix: 1.74 (0.21), residues: 615 sheet: 0.72 (0.36), residues: 166 loop : -0.86 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 186 HIS 0.003 0.001 HIS D 211 PHE 0.009 0.001 PHE B 31 TYR 0.017 0.002 TYR F 102 ARG 0.004 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 468) hydrogen bonds : angle 3.61154 ( 1349) covalent geometry : bond 0.00429 (10072) covalent geometry : angle 0.50927 (13728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.112 Fit side-chains REVERT: A 21 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7295 (mt0) REVERT: B 15 LYS cc_start: 0.8387 (mtmm) cc_final: 0.7905 (mtmt) REVERT: B 97 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8588 (mtm) REVERT: C 15 LYS cc_start: 0.8345 (mtmm) cc_final: 0.7896 (mtmt) REVERT: D 208 LYS cc_start: 0.5813 (OUTLIER) cc_final: 0.5503 (mtmm) REVERT: F 193 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7617 (mtmt) outliers start: 27 outliers final: 17 residues processed: 140 average time/residue: 0.2278 time to fit residues: 45.1024 Evaluate side-chains 136 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 135 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 118 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 87 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.140617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.114314 restraints weight = 19183.808| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.08 r_work: 0.2884 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10072 Z= 0.117 Angle : 0.440 5.308 13728 Z= 0.238 Chirality : 0.041 0.174 1607 Planarity : 0.003 0.044 1751 Dihedral : 3.630 15.209 1402 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.01 % Favored : 96.83 % Rotamer: Outliers : 2.62 % Allowed : 16.13 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1296 helix: 1.86 (0.21), residues: 615 sheet: 0.73 (0.36), residues: 171 loop : -0.82 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 186 HIS 0.002 0.001 HIS E 180 PHE 0.007 0.001 PHE D 157 TYR 0.013 0.001 TYR B 102 ARG 0.003 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.02911 ( 468) hydrogen bonds : angle 3.43596 ( 1349) covalent geometry : bond 0.00288 (10072) covalent geometry : angle 0.43978 (13728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.143 Fit side-chains REVERT: A 21 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: B 15 LYS cc_start: 0.8425 (mtmm) cc_final: 0.7906 (mtmt) REVERT: C 15 LYS cc_start: 0.8315 (mtmm) cc_final: 0.7925 (mtmt) REVERT: D 173 LYS cc_start: 0.6718 (mmtp) cc_final: 0.5783 (tptt) REVERT: D 208 LYS cc_start: 0.5830 (OUTLIER) cc_final: 0.5517 (mtmm) REVERT: F 193 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7541 (mtmt) outliers start: 24 outliers final: 18 residues processed: 147 average time/residue: 0.2151 time to fit residues: 45.3791 Evaluate side-chains 143 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 103 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.135756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.125021 restraints weight = 17429.741| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 0.88 r_work: 0.2922 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 10072 Z= 0.247 Angle : 0.579 7.238 13728 Z= 0.307 Chirality : 0.047 0.254 1607 Planarity : 0.004 0.046 1751 Dihedral : 4.185 17.225 1402 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.79 % Favored : 96.06 % Rotamer: Outliers : 3.46 % Allowed : 14.76 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1296 helix: 1.36 (0.21), residues: 614 sheet: 0.37 (0.37), residues: 163 loop : -0.89 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 37 HIS 0.005 0.001 HIS A 24 PHE 0.011 0.002 PHE B 31 TYR 0.019 0.002 TYR B 102 ARG 0.005 0.001 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 468) hydrogen bonds : angle 3.86629 ( 1349) covalent geometry : bond 0.00628 (10072) covalent geometry : angle 0.57913 (13728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.061 Fit side-chains REVERT: A 21 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: B 15 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8128 (mtmt) REVERT: B 97 MET cc_start: 0.9082 (ptp) cc_final: 0.8643 (mtm) REVERT: B 139 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8072 (mptt) REVERT: C 15 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8136 (mtmt) REVERT: D 43 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8207 (tp) outliers start: 32 outliers final: 23 residues processed: 150 average time/residue: 0.2214 time to fit residues: 46.1320 Evaluate side-chains 152 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain F residue 168 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.138474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.119373 restraints weight = 16674.327| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.03 r_work: 0.2901 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10072 Z= 0.114 Angle : 0.445 5.346 13728 Z= 0.241 Chirality : 0.040 0.177 1607 Planarity : 0.004 0.045 1751 Dihedral : 3.772 15.642 1402 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.94 % Favored : 96.91 % Rotamer: Outliers : 3.14 % Allowed : 15.39 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.23), residues: 1296 helix: 1.74 (0.21), residues: 608 sheet: 0.53 (0.36), residues: 171 loop : -0.87 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 37 HIS 0.002 0.001 HIS E 180 PHE 0.008 0.001 PHE C 157 TYR 0.013 0.001 TYR F 102 ARG 0.005 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 468) hydrogen bonds : angle 3.55404 ( 1349) covalent geometry : bond 0.00278 (10072) covalent geometry : angle 0.44453 (13728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.024 Fit side-chains REVERT: A 21 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7270 (mt0) REVERT: B 15 LYS cc_start: 0.8480 (mtmm) cc_final: 0.7982 (mtmt) REVERT: B 97 MET cc_start: 0.9040 (ptp) cc_final: 0.8549 (mtm) REVERT: B 139 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7946 (mptt) REVERT: C 15 LYS cc_start: 0.8384 (mtmm) cc_final: 0.7967 (mtpt) REVERT: D 173 LYS cc_start: 0.6896 (mmtp) cc_final: 0.5951 (tptt) outliers start: 29 outliers final: 21 residues processed: 143 average time/residue: 0.2346 time to fit residues: 46.3796 Evaluate side-chains 142 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 168 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 0.4980 chunk 74 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 114 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.141080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.122487 restraints weight = 12885.122| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 0.91 r_work: 0.2921 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10072 Z= 0.088 Angle : 0.411 4.954 13728 Z= 0.223 Chirality : 0.039 0.151 1607 Planarity : 0.003 0.043 1751 Dihedral : 3.440 14.612 1402 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.01 % Favored : 96.83 % Rotamer: Outliers : 2.41 % Allowed : 15.71 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1296 helix: 2.04 (0.21), residues: 606 sheet: 0.74 (0.38), residues: 167 loop : -0.87 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 37 HIS 0.002 0.000 HIS E 180 PHE 0.007 0.001 PHE C 157 TYR 0.012 0.001 TYR F 102 ARG 0.006 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.02590 ( 468) hydrogen bonds : angle 3.37498 ( 1349) covalent geometry : bond 0.00202 (10072) covalent geometry : angle 0.41077 (13728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.096 Fit side-chains REVERT: A 21 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: B 15 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8010 (mtmt) REVERT: C 15 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8017 (mtpt) REVERT: C 104 ARG cc_start: 0.7373 (mtt-85) cc_final: 0.7167 (mtt-85) REVERT: C 190 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.8076 (ttp80) REVERT: D 43 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8164 (tp) outliers start: 22 outliers final: 17 residues processed: 140 average time/residue: 0.2048 time to fit residues: 41.4940 Evaluate side-chains 139 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 135 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.139031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.119963 restraints weight = 13826.381| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 0.95 r_work: 0.2931 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10072 Z= 0.120 Angle : 0.445 5.360 13728 Z= 0.239 Chirality : 0.041 0.210 1607 Planarity : 0.003 0.044 1751 Dihedral : 3.544 14.682 1402 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.09 % Favored : 96.75 % Rotamer: Outliers : 2.30 % Allowed : 15.60 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1296 helix: 1.97 (0.21), residues: 608 sheet: 0.57 (0.36), residues: 171 loop : -0.81 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 37 HIS 0.002 0.001 HIS A 24 PHE 0.008 0.001 PHE C 157 TYR 0.014 0.001 TYR F 102 ARG 0.006 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.02952 ( 468) hydrogen bonds : angle 3.44816 ( 1349) covalent geometry : bond 0.00296 (10072) covalent geometry : angle 0.44527 (13728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.113 Fit side-chains REVERT: A 21 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7298 (mt0) REVERT: B 15 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8003 (mtmt) REVERT: B 97 MET cc_start: 0.8996 (ptp) cc_final: 0.8446 (mtm) REVERT: C 15 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8017 (mtpt) REVERT: D 43 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8145 (tp) REVERT: D 173 LYS cc_start: 0.6824 (mmtp) cc_final: 0.5916 (tptt) outliers start: 21 outliers final: 19 residues processed: 142 average time/residue: 0.2328 time to fit residues: 46.6375 Evaluate side-chains 144 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 135 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.140643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.123403 restraints weight = 16340.910| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 0.94 r_work: 0.2942 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10072 Z= 0.092 Angle : 0.413 4.988 13728 Z= 0.224 Chirality : 0.040 0.174 1607 Planarity : 0.003 0.043 1751 Dihedral : 3.397 14.563 1402 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.86 % Favored : 96.99 % Rotamer: Outliers : 2.41 % Allowed : 15.50 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.23), residues: 1296 helix: 2.11 (0.21), residues: 606 sheet: 0.68 (0.37), residues: 169 loop : -0.79 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 37 HIS 0.002 0.000 HIS E 180 PHE 0.007 0.001 PHE C 157 TYR 0.012 0.001 TYR F 102 ARG 0.006 0.000 ARG B 104 Details of bonding type rmsd hydrogen bonds : bond 0.02632 ( 468) hydrogen bonds : angle 3.36055 ( 1349) covalent geometry : bond 0.00216 (10072) covalent geometry : angle 0.41285 (13728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4673.59 seconds wall clock time: 81 minutes 45.20 seconds (4905.20 seconds total)