Starting phenix.real_space_refine on Thu Sep 18 13:56:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e5g_47526/09_2025/9e5g_47526.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e5g_47526/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9e5g_47526/09_2025/9e5g_47526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e5g_47526/09_2025/9e5g_47526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e5g_47526/09_2025/9e5g_47526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e5g_47526/09_2025/9e5g_47526.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TYR:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 9, 'PHE:plan': 1, '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: {'TYR:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 9, 'PHE:plan': 1, '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, 'ASP:plan': 4, 'GLU:plan': 7, 'PHE:plan': 1, 'ARG:plan': 2} 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, 'ASP:plan': 4, 'GLU:plan': 7, 'PHE:plan': 1, 'ARG:plan': 2} 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, 'PHE:plan': 1, 'ARG: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, 'ASP:plan': 3, 'GLU:plan': 7, 'PHE:plan': 1, 'ARG:plan': 2} 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: {'TYR:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 8, 'PHE:plan': 1, '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: {'TYR:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 6, 'PHE:plan': 1, 'ARG:plan': 1, 'HIS: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: 3.13, per 1000 atoms: 0.32 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: 0.76 Conformation dependent library (CDL) restraints added in 324.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 1.61 Time building geometry restraints manager: 0.96 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: 0.010 Normalize map: mean=0, sd=1: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (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 ARG 0.005 0.000 ARG E 95 TYR 0.014 0.001 TYR E 102 PHE 0.007 0.001 PHE C 157 TRP 0.004 0.001 TRP E 216 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00314 (10072) covalent geometry : angle 0.50152 (13728) hydrogen bonds : bond 0.14814 ( 468) hydrogen bonds : angle 4.36251 ( 1349) *********************** 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 : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.7682 (mt0) cc_final: 0.7443 (tt0) REVERT: C 53 ARG cc_start: 0.6925 (mtm-85) cc_final: 0.5817 (mtp180) REVERT: E 47 LYS cc_start: 0.6329 (mtpt) cc_final: 0.5530 (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: 0.1114 time to fit residues: 21.2306 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 : 0.365 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.149080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.129999 restraints weight = 17185.696| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.04 r_work: 0.3062 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10072 Z= 0.151 Angle : 0.525 5.844 13728 Z= 0.282 Chirality : 0.042 0.186 1607 Planarity : 0.004 0.043 1751 Dihedral : 3.687 20.140 1403 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.09 % Favored : 96.75 % Rotamer: Outliers : 1.78 % Allowed : 17.59 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.23), residues: 1296 helix: 1.52 (0.21), residues: 628 sheet: 0.94 (0.37), residues: 172 loop : -0.94 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 147 TYR 0.018 0.002 TYR F 102 PHE 0.011 0.002 PHE A 31 TRP 0.008 0.001 TRP A 37 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00343 (10072) covalent geometry : angle 0.52549 (13728) hydrogen bonds : bond 0.03001 ( 468) hydrogen bonds : angle 3.73727 ( 1349) *********************** 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 131 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.381 Fit side-chains REVERT: A 21 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7247 (mt0) REVERT: D 59 MET cc_start: 0.8656 (mmp) cc_final: 0.8385 (mmp) REVERT: E 47 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7482 (mmtm) REVERT: E 100 MET cc_start: 0.8805 (tmm) cc_final: 0.8594 (ttt) REVERT: E 130 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7950 (mm-30) outliers start: 16 outliers final: 8 residues processed: 129 average time/residue: 0.0848 time to fit residues: 16.1310 Evaluate side-chains 113 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 113 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.142876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.119586 restraints weight = 14003.658| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.03 r_work: 0.3027 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10072 Z= 0.132 Angle : 0.479 5.259 13728 Z= 0.260 Chirality : 0.042 0.179 1607 Planarity : 0.004 0.044 1751 Dihedral : 3.601 14.263 1402 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.01 % Favored : 96.83 % Rotamer: Outliers : 1.78 % Allowed : 17.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.23), residues: 1296 helix: 1.91 (0.22), residues: 615 sheet: 0.81 (0.36), residues: 176 loop : -0.83 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 147 TYR 0.013 0.001 TYR C 102 PHE 0.010 0.001 PHE B 209 TRP 0.006 0.001 TRP E 186 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00313 (10072) covalent geometry : angle 0.47915 (13728) hydrogen bonds : bond 0.04021 ( 468) hydrogen bonds : angle 3.48459 ( 1349) *********************** 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 137 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.389 Fit side-chains REVERT: A 21 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7158 (mt0) REVERT: A 130 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7696 (mm-30) REVERT: A 193 LYS cc_start: 0.7646 (mtpp) cc_final: 0.7293 (mtmt) REVERT: B 15 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7853 (mtpt) REVERT: C 15 LYS cc_start: 0.8277 (mtmm) cc_final: 0.7810 (mtmt) REVERT: D 173 LYS cc_start: 0.6717 (mmtp) cc_final: 0.5879 (tptt) REVERT: E 130 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7721 (mm-30) outliers start: 16 outliers final: 13 residues processed: 134 average time/residue: 0.0877 time to fit residues: 17.4833 Evaluate side-chains 123 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 98 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 C residue 135 ASP 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 103 VAL 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 17 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 87 optimal weight: 0.0470 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.144116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.121367 restraints weight = 13119.718| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.50 r_work: 0.3034 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10072 Z= 0.085 Angle : 0.406 4.966 13728 Z= 0.220 Chirality : 0.040 0.158 1607 Planarity : 0.003 0.044 1751 Dihedral : 3.356 14.280 1402 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.86 % Favored : 96.99 % Rotamer: Outliers : 2.09 % Allowed : 17.49 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.23), residues: 1296 helix: 1.87 (0.21), residues: 630 sheet: 0.93 (0.36), residues: 176 loop : -0.94 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.013 0.001 TYR B 102 PHE 0.007 0.001 PHE C 157 TRP 0.005 0.001 TRP E 186 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00193 (10072) covalent geometry : angle 0.40615 (13728) hydrogen bonds : bond 0.02488 ( 468) hydrogen bonds : angle 3.26914 ( 1349) *********************** 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 137 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.342 Fit side-chains REVERT: A 21 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7125 (mt0) REVERT: A 130 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 193 LYS cc_start: 0.7669 (mtpp) cc_final: 0.7333 (mtmt) REVERT: B 15 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7886 (mtmt) REVERT: C 15 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7884 (mtmt) REVERT: D 15 LYS cc_start: 0.8604 (mtmt) cc_final: 0.8346 (mtmt) REVERT: D 173 LYS cc_start: 0.6644 (mmtp) cc_final: 0.5895 (tptt) REVERT: E 130 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7795 (mm-30) REVERT: F 96 MET cc_start: 0.8785 (mtm) cc_final: 0.8449 (mtp) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 0.0844 time to fit residues: 16.9699 Evaluate side-chains 127 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 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 103 VAL Chi-restraints excluded: chain E residue 135 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 109 optimal weight: 0.0070 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.142633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.122790 restraints weight = 18352.246| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.17 r_work: 0.2914 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10072 Z= 0.096 Angle : 0.417 5.002 13728 Z= 0.224 Chirality : 0.040 0.166 1607 Planarity : 0.003 0.043 1751 Dihedral : 3.314 15.516 1402 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.94 % Favored : 96.91 % Rotamer: Outliers : 2.51 % Allowed : 16.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.23), residues: 1296 helix: 2.10 (0.21), residues: 615 sheet: 1.07 (0.36), residues: 172 loop : -0.77 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.013 0.001 TYR F 102 PHE 0.007 0.001 PHE B 209 TRP 0.004 0.001 TRP E 186 HIS 0.002 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00226 (10072) covalent geometry : angle 0.41673 (13728) hydrogen bonds : bond 0.02665 ( 468) hydrogen bonds : angle 3.25444 ( 1349) *********************** 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 145 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.388 Fit side-chains REVERT: A 21 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7227 (mt0) REVERT: A 130 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 193 LYS cc_start: 0.7824 (mtpp) cc_final: 0.7462 (mtmt) REVERT: B 15 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7997 (mtmt) REVERT: C 15 LYS cc_start: 0.8372 (mtmm) cc_final: 0.7969 (mtmt) REVERT: D 173 LYS cc_start: 0.6663 (mmtp) cc_final: 0.5847 (tptt) REVERT: D 208 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5557 (mtmm) REVERT: E 102 TYR cc_start: 0.8759 (p90) cc_final: 0.8553 (p90) REVERT: E 130 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7921 (mm-30) outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 0.0887 time to fit residues: 18.2793 Evaluate side-chains 139 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 21 GLN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER 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 20 optimal weight: 0.6980 chunk 110 optimal weight: 0.0000 chunk 91 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.142966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.119690 restraints weight = 14028.097| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.71 r_work: 0.3009 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10072 Z= 0.097 Angle : 0.416 5.095 13728 Z= 0.224 Chirality : 0.040 0.167 1607 Planarity : 0.003 0.044 1751 Dihedral : 3.328 14.497 1402 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.01 % Favored : 96.83 % Rotamer: Outliers : 2.51 % Allowed : 16.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.23), residues: 1296 helix: 2.06 (0.21), residues: 615 sheet: 0.95 (0.36), residues: 172 loop : -0.76 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 53 TYR 0.013 0.001 TYR B 102 PHE 0.009 0.001 PHE E 209 TRP 0.005 0.001 TRP A 37 HIS 0.002 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00231 (10072) covalent geometry : angle 0.41609 (13728) hydrogen bonds : bond 0.02581 ( 468) hydrogen bonds : angle 3.24090 ( 1349) *********************** 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 148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.377 Fit side-chains REVERT: A 21 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7158 (mt0) REVERT: A 130 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 193 LYS cc_start: 0.7656 (mtpp) cc_final: 0.7318 (mtmt) REVERT: B 15 LYS cc_start: 0.8313 (mtmm) cc_final: 0.7865 (mtmt) REVERT: C 15 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7838 (mtmt) REVERT: D 173 LYS cc_start: 0.6503 (mmtp) cc_final: 0.5821 (tptp) REVERT: D 208 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.5391 (mtmm) REVERT: E 130 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7854 (mt-10) outliers start: 23 outliers final: 17 residues processed: 142 average time/residue: 0.0841 time to fit residues: 17.6407 Evaluate side-chains 142 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 21 GLN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 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 133 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.142574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.120839 restraints weight = 9634.970| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.14 r_work: 0.3051 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10072 Z= 0.101 Angle : 0.418 5.052 13728 Z= 0.225 Chirality : 0.040 0.195 1607 Planarity : 0.003 0.044 1751 Dihedral : 3.343 15.838 1402 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 2.62 % Allowed : 16.75 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.23), residues: 1296 helix: 2.08 (0.21), residues: 615 sheet: 0.92 (0.37), residues: 170 loop : -0.76 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.014 0.001 TYR F 102 PHE 0.007 0.001 PHE B 157 TRP 0.004 0.001 TRP E 186 HIS 0.002 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00242 (10072) covalent geometry : angle 0.41804 (13728) hydrogen bonds : bond 0.02666 ( 468) hydrogen bonds : angle 3.26747 ( 1349) *********************** 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: 24 poor density : 128 time to evaluate : 0.281 Fit side-chains REVERT: A 21 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7258 (mt0) REVERT: A 130 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 193 LYS cc_start: 0.7675 (mtpp) cc_final: 0.7318 (mtmt) REVERT: B 15 LYS cc_start: 0.8370 (mtmm) cc_final: 0.7889 (mtmt) REVERT: C 15 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7874 (mtmt) REVERT: C 204 ASP cc_start: 0.7028 (m-30) cc_final: 0.6827 (m-30) REVERT: D 173 LYS cc_start: 0.6492 (mmtp) cc_final: 0.5779 (tptt) REVERT: D 208 LYS cc_start: 0.5801 (OUTLIER) cc_final: 0.5493 (mtmm) REVERT: E 130 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7938 (mt-10) REVERT: F 193 LYS cc_start: 0.7871 (mtmt) cc_final: 0.7542 (mtmt) outliers start: 24 outliers final: 22 residues processed: 147 average time/residue: 0.0989 time to fit residues: 20.9208 Evaluate side-chains 151 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 A residue 152 THR Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 135 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 127 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 114 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.140301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123781 restraints weight = 18142.459| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.06 r_work: 0.2910 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10072 Z= 0.116 Angle : 0.438 5.152 13728 Z= 0.235 Chirality : 0.041 0.187 1607 Planarity : 0.003 0.044 1751 Dihedral : 3.442 14.185 1402 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.25 % Favored : 96.60 % Rotamer: Outliers : 2.93 % Allowed : 16.23 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.23), residues: 1296 helix: 2.02 (0.21), residues: 615 sheet: 0.82 (0.36), residues: 170 loop : -0.79 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.015 0.001 TYR F 102 PHE 0.008 0.001 PHE C 157 TRP 0.005 0.001 TRP A 37 HIS 0.002 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00285 (10072) covalent geometry : angle 0.43844 (13728) hydrogen bonds : bond 0.02869 ( 468) hydrogen bonds : angle 3.34161 ( 1349) *********************** 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 156 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.369 Fit side-chains REVERT: A 21 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: A 130 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7966 (mm-30) REVERT: A 193 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7567 (mtmt) REVERT: B 15 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8071 (mtmt) REVERT: B 97 MET cc_start: 0.8966 (ptp) cc_final: 0.8423 (mtm) REVERT: C 15 LYS cc_start: 0.8438 (mtmm) cc_final: 0.8036 (mtmt) REVERT: C 104 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7550 (mtm-85) REVERT: C 204 ASP cc_start: 0.7253 (m-30) cc_final: 0.7050 (m-30) REVERT: D 173 LYS cc_start: 0.6803 (mmtp) cc_final: 0.6136 (tptt) REVERT: D 208 LYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5843 (mtmm) REVERT: E 130 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8131 (mt-10) REVERT: F 193 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7792 (mtmt) outliers start: 27 outliers final: 22 residues processed: 150 average time/residue: 0.0932 time to fit residues: 20.1869 Evaluate side-chains 151 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 A residue 152 THR Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain E residue 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 135 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.0870 chunk 101 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 0.0470 chunk 93 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.142270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.125622 restraints weight = 12507.487| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.80 r_work: 0.3010 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10072 Z= 0.086 Angle : 0.403 4.959 13728 Z= 0.218 Chirality : 0.040 0.158 1607 Planarity : 0.003 0.044 1751 Dihedral : 3.279 14.388 1402 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.70 % Favored : 97.14 % Rotamer: Outliers : 2.72 % Allowed : 16.65 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.23), residues: 1296 helix: 2.14 (0.21), residues: 615 sheet: 1.00 (0.38), residues: 166 loop : -0.77 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 68 TYR 0.012 0.001 TYR F 102 PHE 0.007 0.001 PHE C 157 TRP 0.004 0.001 TRP E 186 HIS 0.002 0.000 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00199 (10072) covalent geometry : angle 0.40286 (13728) hydrogen bonds : bond 0.02497 ( 468) hydrogen bonds : angle 3.24816 ( 1349) *********************** 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: 25 poor density : 127 time to evaluate : 0.260 Fit side-chains REVERT: A 21 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7354 (mt0) REVERT: A 130 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7845 (mm-30) REVERT: B 15 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8021 (mtmt) REVERT: C 15 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8007 (mtmt) REVERT: C 104 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7384 (mtm-85) REVERT: D 173 LYS cc_start: 0.6696 (mmtp) cc_final: 0.6160 (tptt) REVERT: D 208 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5752 (mtmm) REVERT: E 130 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7991 (mt-10) REVERT: F 193 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7719 (mtmt) outliers start: 25 outliers final: 21 residues processed: 148 average time/residue: 0.0940 time to fit residues: 19.6600 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 : 0.307 ------------------------------------------------------------------------------- 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 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 C residue 195 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 135 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 60 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.138583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.120136 restraints weight = 16516.485| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 0.95 r_work: 0.2919 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10072 Z= 0.138 Angle : 0.464 5.457 13728 Z= 0.248 Chirality : 0.042 0.206 1607 Planarity : 0.003 0.044 1751 Dihedral : 3.554 14.674 1402 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.40 % Favored : 96.45 % Rotamer: Outliers : 2.83 % Allowed : 16.23 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.23), residues: 1296 helix: 1.95 (0.21), residues: 615 sheet: 0.72 (0.36), residues: 170 loop : -0.78 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 68 TYR 0.017 0.002 TYR F 102 PHE 0.008 0.001 PHE B 157 TRP 0.006 0.001 TRP A 37 HIS 0.003 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00349 (10072) covalent geometry : angle 0.46448 (13728) hydrogen bonds : bond 0.03127 ( 468) hydrogen bonds : angle 3.42162 ( 1349) ********************** 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 150 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.292 Fit side-chains REVERT: A 21 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7337 (mt0) REVERT: B 15 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8021 (mtmt) REVERT: B 97 MET cc_start: 0.9026 (ptp) cc_final: 0.8532 (mtm) REVERT: C 15 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8076 (mtmt) REVERT: C 104 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7533 (mtm-85) REVERT: D 173 LYS cc_start: 0.6722 (mmtp) cc_final: 0.6041 (tptt) REVERT: D 208 LYS cc_start: 0.6042 (OUTLIER) cc_final: 0.5791 (mtmm) REVERT: E 130 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8065 (mm-30) REVERT: F 193 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7850 (mtmt) outliers start: 26 outliers final: 23 residues processed: 146 average time/residue: 0.1055 time to fit residues: 21.6689 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 : 0.387 ------------------------------------------------------------------------------- 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 75 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 152 THR 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 130 GLU Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 135 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 114 optimal weight: 0.0060 chunk 51 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.142006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.123507 restraints weight = 16550.173| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 0.99 r_work: 0.2962 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10072 Z= 0.087 Angle : 0.401 4.977 13728 Z= 0.217 Chirality : 0.040 0.155 1607 Planarity : 0.003 0.044 1751 Dihedral : 3.287 14.247 1402 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 2.51 % Allowed : 16.65 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.23), residues: 1296 helix: 2.13 (0.21), residues: 615 sheet: 0.90 (0.38), residues: 166 loop : -0.76 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 95 TYR 0.011 0.001 TYR F 102 PHE 0.007 0.001 PHE C 157 TRP 0.005 0.001 TRP B 37 HIS 0.002 0.000 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00201 (10072) covalent geometry : angle 0.40109 (13728) hydrogen bonds : bond 0.02471 ( 468) hydrogen bonds : angle 3.27093 ( 1349) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2336.88 seconds wall clock time: 40 minutes 38.40 seconds (2438.40 seconds total)