Starting phenix.real_space_refine on Sun Jun 15 11:28:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e5g_47526/06_2025/9e5g_47526.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e5g_47526/06_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_47526/06_2025/9e5g_47526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e5g_47526/06_2025/9e5g_47526.map" model { file = "/net/cci-nas-00/data/ceres_data/9e5g_47526/06_2025/9e5g_47526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e5g_47526/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.85, per 1000 atoms: 0.89 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: 2.44 Conformation dependent library (CDL) restraints added in 1.7 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: 2.63 Time building geometry restraints manager: 2.80 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: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.600 Find NCS groups from input model: 0.590 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.570 ------------------------------------------------------------------------------- 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 : 0.943 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: 0.2573 time to fit residues: 49.2331 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 : 1.109 ------------------------------------------------------------------------------- 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: 0.3122 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 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 = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 0.924 Fit side-chains REVERT: A 21 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7211 (mt0) REVERT: D 173 LYS cc_start: 0.6957 (mmtp) cc_final: 0.6324 (tptp) REVERT: E 47 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7442 (mmtm) REVERT: E 100 MET cc_start: 0.8772 (tmm) cc_final: 0.8466 (ttt) outliers start: 15 outliers final: 8 residues processed: 130 average time/residue: 0.1955 time to fit residues: 37.6258 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 : 1.048 ------------------------------------------------------------------------------- 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: 2.9990 chunk 96 optimal weight: 0.1980 chunk 71 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.145048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.125383 restraints weight = 19261.258| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.10 r_work: 0.2973 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 10072 Z= 0.124 Angle : 0.467 5.263 13728 Z= 0.252 Chirality : 0.042 0.310 1607 Planarity : 0.004 0.043 1751 Dihedral : 3.475 14.027 1402 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.86 % Favored : 96.99 % Rotamer: Outliers : 1.88 % Allowed : 17.80 % 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: 1.07 (0.23), residues: 1296 helix: 1.87 (0.22), residues: 632 sheet: 0.79 (0.36), residues: 176 loop : -0.87 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 186 HIS 0.007 0.001 HIS F 24 PHE 0.012 0.001 PHE E 142 TYR 0.012 0.001 TYR C 102 ARG 0.010 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 468) hydrogen bonds : angle 3.39376 ( 1349) covalent geometry : bond 0.00296 (10072) covalent geometry : angle 0.46701 (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 139 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.013 Fit side-chains REVERT: A 21 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: A 115 GLN cc_start: 0.8753 (tt0) cc_final: 0.8227 (tt0) REVERT: A 130 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 193 LYS cc_start: 0.7881 (mtpp) cc_final: 0.7585 (mtmt) REVERT: B 15 LYS cc_start: 0.8300 (mtmm) cc_final: 0.8012 (mtmt) REVERT: C 15 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8033 (mtmt) REVERT: E 47 LYS cc_start: 0.8546 (mtpt) cc_final: 0.7775 (mmtm) outliers start: 17 outliers final: 10 residues processed: 138 average time/residue: 0.1909 time to fit residues: 38.9233 Evaluate side-chains 122 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 195 SER 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 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 133 THR 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: 0.1980 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.141924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.130319 restraints weight = 14430.591| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.50 r_work: 0.3080 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10072 Z= 0.172 Angle : 0.512 6.354 13728 Z= 0.275 Chirality : 0.043 0.227 1607 Planarity : 0.004 0.046 1751 Dihedral : 3.910 14.408 1402 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.71 % Favored : 96.14 % Rotamer: Outliers : 2.72 % Allowed : 16.23 % 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: 0.82 (0.23), residues: 1296 helix: 1.63 (0.21), residues: 615 sheet: 0.73 (0.35), residues: 172 loop : -0.87 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 37 HIS 0.003 0.001 HIS D 24 PHE 0.010 0.001 PHE B 31 TYR 0.018 0.002 TYR B 102 ARG 0.006 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 468) hydrogen bonds : angle 3.66142 ( 1349) covalent geometry : bond 0.00422 (10072) covalent geometry : angle 0.51198 (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 149 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.982 Fit side-chains REVERT: A 21 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7435 (mt0) REVERT: A 130 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7911 (mm-30) REVERT: A 193 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7808 (mtmt) REVERT: B 15 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8108 (mtmt) REVERT: B 97 MET cc_start: 0.9031 (ptp) cc_final: 0.8563 (mtm) REVERT: C 15 LYS cc_start: 0.8429 (mtmm) cc_final: 0.8053 (mtmt) REVERT: F 193 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7741 (mtmt) outliers start: 25 outliers final: 17 residues processed: 141 average time/residue: 0.2244 time to fit residues: 44.4870 Evaluate side-chains 137 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 43 ILE 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 C residue 54 VAL Chi-restraints excluded: chain C residue 83 THR 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 135 ASP 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 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: 0.8980 chunk 38 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.142420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.121904 restraints weight = 20154.816| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.35 r_work: 0.2904 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10072 Z= 0.100 Angle : 0.425 4.930 13728 Z= 0.231 Chirality : 0.040 0.157 1607 Planarity : 0.003 0.044 1751 Dihedral : 3.559 15.279 1402 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.22 % Rotamer: Outliers : 2.09 % Allowed : 16.86 % 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: 1.10 (0.23), residues: 1296 helix: 1.91 (0.21), residues: 615 sheet: 0.90 (0.36), residues: 171 loop : -0.81 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 37 HIS 0.002 0.001 HIS E 180 PHE 0.007 0.001 PHE D 157 TYR 0.012 0.001 TYR F 102 ARG 0.004 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.02737 ( 468) hydrogen bonds : angle 3.37388 ( 1349) covalent geometry : bond 0.00241 (10072) covalent geometry : angle 0.42522 (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 146 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.961 Fit side-chains REVERT: A 21 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7214 (mt0) REVERT: A 130 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 193 LYS cc_start: 0.7715 (mtpp) cc_final: 0.7491 (mtmt) REVERT: B 15 LYS cc_start: 0.8377 (mtmm) cc_final: 0.7946 (mtmt) REVERT: B 97 MET cc_start: 0.9031 (ptp) cc_final: 0.8532 (mtm) REVERT: C 15 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7971 (mtmt) REVERT: D 173 LYS cc_start: 0.6809 (mmtp) cc_final: 0.5885 (tptt) outliers start: 19 outliers final: 13 residues processed: 142 average time/residue: 0.2120 time to fit residues: 42.6495 Evaluate side-chains 135 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 98 VAL 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 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: 4.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 80 optimal weight: 0.0040 chunk 118 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.139063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.118954 restraints weight = 19439.622| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.42 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5792 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= 0.131 Angle : 0.463 5.574 13728 Z= 0.248 Chirality : 0.041 0.193 1607 Planarity : 0.004 0.044 1751 Dihedral : 3.649 15.040 1402 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.25 % Favored : 96.60 % Rotamer: Outliers : 2.72 % Allowed : 15.39 % 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: 0.99 (0.23), residues: 1296 helix: 1.81 (0.21), residues: 615 sheet: 0.75 (0.35), residues: 172 loop : -0.83 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 37 HIS 0.003 0.001 HIS A 24 PHE 0.009 0.001 PHE E 209 TYR 0.015 0.001 TYR B 102 ARG 0.005 0.000 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 468) hydrogen bonds : angle 3.46424 ( 1349) covalent geometry : bond 0.00329 (10072) covalent geometry : angle 0.46301 (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 149 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.986 Fit side-chains REVERT: A 21 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7126 (mt0) REVERT: B 15 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8208 (mtmt) REVERT: B 97 MET cc_start: 0.8980 (ptp) cc_final: 0.8524 (mtm) REVERT: B 139 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7919 (mptt) REVERT: C 15 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8136 (mtmt) REVERT: D 43 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7969 (tp) REVERT: D 173 LYS cc_start: 0.7132 (mmtp) cc_final: 0.6521 (tptt) REVERT: F 193 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7784 (mtmt) outliers start: 25 outliers final: 21 residues processed: 143 average time/residue: 0.2342 time to fit residues: 46.5042 Evaluate side-chains 148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 43 ILE 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 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 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 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 Chi-restraints excluded: chain F residue 168 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 76 optimal weight: 0.0770 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.140724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.122586 restraints weight = 17732.279| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.12 r_work: 0.2897 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10072 Z= 0.099 Angle : 0.417 5.002 13728 Z= 0.226 Chirality : 0.040 0.160 1607 Planarity : 0.003 0.043 1751 Dihedral : 3.474 14.543 1402 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.70 % Favored : 97.14 % Rotamer: Outliers : 2.72 % Allowed : 15.29 % Favored : 81.99 % 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: 1.14 (0.23), residues: 1296 helix: 1.98 (0.21), residues: 615 sheet: 0.85 (0.37), residues: 171 loop : -0.81 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 37 HIS 0.002 0.001 HIS E 180 PHE 0.007 0.001 PHE C 157 TYR 0.012 0.001 TYR F 102 ARG 0.003 0.000 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.02659 ( 468) hydrogen bonds : angle 3.34070 ( 1349) covalent geometry : bond 0.00234 (10072) covalent geometry : angle 0.41730 (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 152 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.092 Fit side-chains REVERT: A 21 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7310 (mt0) REVERT: A 130 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 15 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8041 (mtmt) REVERT: B 97 MET cc_start: 0.9012 (ptp) cc_final: 0.8482 (mtm) REVERT: C 15 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8055 (mtmt) REVERT: C 63 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: C 190 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.8048 (ttp80) REVERT: C 204 ASP cc_start: 0.7177 (m-30) cc_final: 0.6965 (m-30) REVERT: D 173 LYS cc_start: 0.6839 (mmtp) cc_final: 0.5983 (tptt) REVERT: F 193 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7705 (mtmt) outliers start: 25 outliers final: 19 residues processed: 147 average time/residue: 0.2145 time to fit residues: 45.1463 Evaluate side-chains 147 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 43 ILE 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 C residue 54 VAL Chi-restraints excluded: chain C residue 63 GLU 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 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 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: 0.9990 chunk 33 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 107 optimal weight: 0.0570 chunk 54 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.140109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.120966 restraints weight = 16613.640| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.06 r_work: 0.2912 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10072 Z= 0.104 Angle : 0.428 5.095 13728 Z= 0.231 Chirality : 0.040 0.191 1607 Planarity : 0.003 0.043 1751 Dihedral : 3.466 14.375 1402 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.32 % Favored : 96.52 % Rotamer: Outliers : 2.83 % Allowed : 14.66 % Favored : 82.51 % 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: 1.15 (0.23), residues: 1296 helix: 1.99 (0.21), residues: 615 sheet: 0.84 (0.37), residues: 169 loop : -0.81 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 37 HIS 0.002 0.001 HIS E 180 PHE 0.007 0.001 PHE C 157 TYR 0.014 0.001 TYR F 102 ARG 0.006 0.000 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.02773 ( 468) hydrogen bonds : angle 3.34578 ( 1349) covalent geometry : bond 0.00251 (10072) covalent geometry : angle 0.42812 (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 153 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.038 Fit side-chains REVERT: A 21 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: A 130 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7889 (mm-30) REVERT: B 15 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8020 (mtmt) REVERT: B 97 MET cc_start: 0.9011 (ptp) cc_final: 0.8485 (mtm) REVERT: C 15 LYS cc_start: 0.8387 (mtmm) cc_final: 0.8034 (mtmt) REVERT: C 63 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: C 204 ASP cc_start: 0.7109 (m-30) cc_final: 0.6886 (m-30) REVERT: D 43 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8107 (tp) REVERT: D 173 LYS cc_start: 0.6843 (mmtp) cc_final: 0.5933 (tptt) REVERT: F 193 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7676 (mtmt) outliers start: 26 outliers final: 20 residues processed: 148 average time/residue: 0.2109 time to fit residues: 44.7022 Evaluate side-chains 149 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 63 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 195 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 11 optimal weight: 0.0670 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 114 optimal weight: 0.0870 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.142534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.125468 restraints weight = 12857.522| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.84 r_work: 0.2994 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10072 Z= 0.084 Angle : 0.397 4.911 13728 Z= 0.215 Chirality : 0.039 0.155 1607 Planarity : 0.003 0.042 1751 Dihedral : 3.272 13.978 1402 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 2.41 % Allowed : 14.97 % Favored : 82.62 % 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: 1.39 (0.23), residues: 1296 helix: 2.25 (0.21), residues: 608 sheet: 0.98 (0.37), residues: 169 loop : -0.73 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 37 HIS 0.002 0.000 HIS A 155 PHE 0.007 0.001 PHE C 157 TYR 0.011 0.001 TYR B 102 ARG 0.005 0.000 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.02412 ( 468) hydrogen bonds : angle 3.23313 ( 1349) covalent geometry : bond 0.00191 (10072) covalent geometry : angle 0.39684 (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 152 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.057 Fit side-chains REVERT: A 21 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: A 130 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7826 (mm-30) REVERT: B 15 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8058 (mtmt) REVERT: C 15 LYS cc_start: 0.8390 (mtmm) cc_final: 0.8018 (mtmt) REVERT: C 204 ASP cc_start: 0.7235 (m-30) cc_final: 0.7035 (m-30) REVERT: D 173 LYS cc_start: 0.6857 (mmtp) cc_final: 0.6094 (tptt) REVERT: F 193 LYS cc_start: 0.8029 (mtmt) cc_final: 0.7721 (mtmt) outliers start: 22 outliers final: 20 residues processed: 149 average time/residue: 0.2161 time to fit residues: 45.7369 Evaluate side-chains 147 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 54 VAL Chi-restraints excluded: chain D residue 98 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 Chi-restraints excluded: chain F residue 168 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 128 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.140459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.121078 restraints weight = 13782.871| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.14 r_work: 0.2923 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10072 Z= 0.106 Angle : 0.427 5.053 13728 Z= 0.230 Chirality : 0.040 0.187 1607 Planarity : 0.003 0.043 1751 Dihedral : 3.381 14.069 1402 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.17 % Favored : 96.68 % Rotamer: Outliers : 2.72 % Allowed : 14.76 % Favored : 82.51 % 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: 1.34 (0.23), residues: 1296 helix: 2.19 (0.21), residues: 608 sheet: 0.91 (0.37), residues: 170 loop : -0.71 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 37 HIS 0.002 0.001 HIS E 180 PHE 0.007 0.001 PHE C 157 TYR 0.014 0.001 TYR B 102 ARG 0.007 0.000 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.02758 ( 468) hydrogen bonds : angle 3.30517 ( 1349) covalent geometry : bond 0.00256 (10072) covalent geometry : angle 0.42734 (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 155 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.983 Fit side-chains REVERT: A 21 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: A 130 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7845 (mm-30) REVERT: B 15 LYS cc_start: 0.8485 (mtmm) cc_final: 0.7976 (mtmt) REVERT: B 97 MET cc_start: 0.8956 (ptp) cc_final: 0.8392 (mtm) REVERT: B 139 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7943 (mptt) REVERT: C 15 LYS cc_start: 0.8384 (mtmm) cc_final: 0.8023 (mtmt) REVERT: C 204 ASP cc_start: 0.7111 (m-30) cc_final: 0.6861 (m-30) REVERT: D 43 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8106 (tp) REVERT: D 173 LYS cc_start: 0.6774 (mmtp) cc_final: 0.5881 (tptt) REVERT: F 193 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7700 (mtmt) outliers start: 25 outliers final: 20 residues processed: 152 average time/residue: 0.2102 time to fit residues: 45.5933 Evaluate side-chains 148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 195 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.140589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.121800 restraints weight = 16362.631| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 0.99 r_work: 0.2936 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10072 Z= 0.102 Angle : 0.423 5.017 13728 Z= 0.227 Chirality : 0.040 0.179 1607 Planarity : 0.003 0.043 1751 Dihedral : 3.394 14.700 1402 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.86 % Favored : 96.99 % Rotamer: Outliers : 2.93 % Allowed : 14.66 % Favored : 82.41 % 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: 1.35 (0.23), residues: 1296 helix: 2.19 (0.21), residues: 608 sheet: 0.91 (0.37), residues: 169 loop : -0.70 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 186 HIS 0.002 0.001 HIS E 180 PHE 0.007 0.001 PHE C 157 TYR 0.014 0.001 TYR B 102 ARG 0.005 0.000 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.02705 ( 468) hydrogen bonds : angle 3.29846 ( 1349) covalent geometry : bond 0.00246 (10072) covalent geometry : angle 0.42253 (13728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4782.59 seconds wall clock time: 82 minutes 40.77 seconds (4960.77 seconds total)