Starting phenix.real_space_refine on Fri Sep 19 08:04:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rml_19363/09_2025/8rml_19363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rml_19363/09_2025/8rml_19363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rml_19363/09_2025/8rml_19363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rml_19363/09_2025/8rml_19363.map" model { file = "/net/cci-nas-00/data/ceres_data/8rml_19363/09_2025/8rml_19363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rml_19363/09_2025/8rml_19363.cif" } resolution = 3.84 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15752 2.51 5 N 4272 2.21 5 O 4302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s 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: 24454 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2053 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "L" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2053 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain breaks: 1 Chain: "C" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2243 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 14, 'TRANS': 273} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2159 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 14, 'TRANS': 254} Chain: "E" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2182 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain: "F" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2167 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 14, 'TRANS': 255} Chain: "G" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2159 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 14, 'TRANS': 254} Chain: "H" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2150 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain: "I" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2150 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain: "J" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1801 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "K" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1871 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 8, 'TRANS': 231} Chain breaks: 1 Chain: "M" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Time building chain proxies: 6.00, per 1000 atoms: 0.25 Number of scatterers: 24454 At special positions: 0 Unit cell: (134.106, 151.032, 157.542, 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 128 16.00 O 4302 8.00 N 4272 7.00 C 15752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.02 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5868 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 8 sheets defined 73.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 15 through 38 Processing helix chain 'A' and resid 48 through 70 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.694A pdb=" N THR A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.848A pdb=" N ARG A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 137 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 169 through 208 removed outlier: 4.263A pdb=" N VAL A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 252 removed outlier: 3.806A pdb=" N CYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 4.069A pdb=" N ASP A 274 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 275' Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'B' and resid 6 through 15 Processing helix chain 'B' and resid 15 through 38 Processing helix chain 'B' and resid 48 through 70 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.694A pdb=" N THR B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 3.848A pdb=" N ARG B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 134 through 137 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 169 through 208 removed outlier: 4.263A pdb=" N VAL B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 252 removed outlier: 3.806A pdb=" N CYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 4.068A pdb=" N ASP B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 275' Processing helix chain 'C' and resid 20 through 43 removed outlier: 3.579A pdb=" N VAL C 28 " --> pdb=" O PHE C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 76 removed outlier: 3.554A pdb=" N ILE C 61 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Proline residue: C 64 - end of helix removed outlier: 3.534A pdb=" N ASN C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 90 removed outlier: 4.226A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 81 " --> pdb=" O ASN C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 110 removed outlier: 3.582A pdb=" N GLY C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.847A pdb=" N VAL C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 removed outlier: 3.997A pdb=" N CYS C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.503A pdb=" N LEU C 141 " --> pdb=" O PRO C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.581A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 210 removed outlier: 3.929A pdb=" N GLU C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 252 Processing helix chain 'C' and resid 257 through 267 removed outlier: 3.531A pdb=" N GLU C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 281 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'D' and resid 38 through 42 Processing helix chain 'D' and resid 52 through 76 Proline residue: D 64 - end of helix removed outlier: 3.529A pdb=" N ASN D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.501A pdb=" N CYS D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 111 removed outlier: 4.073A pdb=" N THR D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.858A pdb=" N ILE D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 133 removed outlier: 3.526A pdb=" N CYS D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 169 through 210 removed outlier: 3.533A pdb=" N LYS D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS D 207 " --> pdb=" O LYS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 252 removed outlier: 3.545A pdb=" N GLU D 236 " --> pdb=" O GLN D 232 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 267 Processing helix chain 'D' and resid 274 through 281 removed outlier: 3.756A pdb=" N ILE D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 52 through 76 Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 77 through 89 removed outlier: 3.871A pdb=" N ASN E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 109 removed outlier: 3.703A pdb=" N THR E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 102 " --> pdb=" O PRO E 98 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.658A pdb=" N ILE E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 210 removed outlier: 3.767A pdb=" N ARG E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 252 removed outlier: 3.595A pdb=" N ALA E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN E 226 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU E 242 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG E 249 " --> pdb=" O ASN E 245 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE E 250 " --> pdb=" O ASN E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 removed outlier: 4.189A pdb=" N GLU E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 280 Processing helix chain 'E' and resid 297 through 304 Processing helix chain 'F' and resid 38 through 42 removed outlier: 3.583A pdb=" N VAL F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 38 through 42' Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 61 through 76 Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.502A pdb=" N CYS F 86 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 125 removed outlier: 4.255A pdb=" N THR F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU F 102 " --> pdb=" O PRO F 98 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 110 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL F 112 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Proline residue: F 114 - end of helix removed outlier: 3.916A pdb=" N ILE F 120 " --> pdb=" O THR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 152 through 159 Processing helix chain 'F' and resid 160 through 163 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 209 removed outlier: 3.810A pdb=" N ARG F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 252 removed outlier: 3.582A pdb=" N TYR F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN F 226 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG F 249 " --> pdb=" O ASN F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 267 removed outlier: 3.926A pdb=" N GLU F 262 " --> pdb=" O LYS F 258 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 264 " --> pdb=" O ASP F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 297 through 304 Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'G' and resid 52 through 76 removed outlier: 4.079A pdb=" N VAL G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.562A pdb=" N HIS G 88 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG G 90 " --> pdb=" O CYS G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 111 removed outlier: 3.931A pdb=" N THR G 99 " --> pdb=" O SER G 95 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU G 102 " --> pdb=" O PRO G 98 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.950A pdb=" N ILE G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 132 Processing helix chain 'G' and resid 133 through 136 removed outlier: 3.695A pdb=" N VAL G 136 " --> pdb=" O SER G 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 133 through 136' Processing helix chain 'G' and resid 152 through 159 removed outlier: 3.834A pdb=" N ILE G 156 " --> pdb=" O HIS G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 169 through 210 Processing helix chain 'G' and resid 213 through 252 removed outlier: 4.023A pdb=" N ALA G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN G 226 " --> pdb=" O GLN G 222 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 237 " --> pdb=" O ARG G 233 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU G 242 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN G 246 " --> pdb=" O LEU G 242 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG G 249 " --> pdb=" O ASN G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 267 removed outlier: 4.030A pdb=" N GLU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'H' and resid 52 through 76 Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 79 through 89 removed outlier: 3.527A pdb=" N GLN H 87 " --> pdb=" O VAL H 83 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 111 removed outlier: 4.075A pdb=" N THR H 99 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU H 102 " --> pdb=" O PRO H 98 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 removed outlier: 3.592A pdb=" N ILE H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 133 Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 152 through 159 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 210 removed outlier: 3.779A pdb=" N ARG H 181 " --> pdb=" O SER H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 252 removed outlier: 3.552A pdb=" N VAL H 237 " --> pdb=" O ARG H 233 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU H 242 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG H 249 " --> pdb=" O ASN H 245 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE H 250 " --> pdb=" O ASN H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 267 removed outlier: 4.258A pdb=" N GLU H 262 " --> pdb=" O LYS H 258 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU H 263 " --> pdb=" O ASP H 259 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE H 264 " --> pdb=" O ASP H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 297 through 304 Processing helix chain 'I' and resid 52 through 76 Proline residue: I 64 - end of helix removed outlier: 3.689A pdb=" N ILE I 73 " --> pdb=" O PHE I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 90 removed outlier: 3.840A pdb=" N ASN I 81 " --> pdb=" O ASN I 77 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N CYS I 86 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN I 87 " --> pdb=" O VAL I 83 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 111 removed outlier: 3.582A pdb=" N THR I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LEU I 102 " --> pdb=" O PRO I 98 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU I 103 " --> pdb=" O THR I 99 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER I 104 " --> pdb=" O PHE I 100 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER I 105 " --> pdb=" O LEU I 101 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE I 106 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY I 108 " --> pdb=" O SER I 104 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 removed outlier: 3.645A pdb=" N VAL I 119 " --> pdb=" O VAL I 115 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE I 120 " --> pdb=" O THR I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 132 Processing helix chain 'I' and resid 137 through 141 Processing helix chain 'I' and resid 152 through 159 removed outlier: 3.543A pdb=" N ILE I 156 " --> pdb=" O HIS I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 210 removed outlier: 3.522A pdb=" N VAL I 176 " --> pdb=" O PHE I 172 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE I 192 " --> pdb=" O GLY I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 252 removed outlier: 4.467A pdb=" N GLN I 229 " --> pdb=" O ALA I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 267 removed outlier: 3.933A pdb=" N GLU I 262 " --> pdb=" O LYS I 258 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU I 263 " --> pdb=" O ASP I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'J' and resid 52 through 76 removed outlier: 3.647A pdb=" N TYR J 56 " --> pdb=" O ARG J 52 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE J 61 " --> pdb=" O GLY J 57 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix removed outlier: 3.671A pdb=" N LEU J 68 " --> pdb=" O PRO J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 Processing helix chain 'J' and resid 99 through 110 removed outlier: 3.542A pdb=" N ARG J 109 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'J' and resid 125 through 135 removed outlier: 3.502A pdb=" N VAL J 129 " --> pdb=" O GLY J 125 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS J 130 " --> pdb=" O GLU J 126 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU J 132 " --> pdb=" O TYR J 128 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER J 133 " --> pdb=" O VAL J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 160 Processing helix chain 'J' and resid 170 through 210 removed outlier: 3.667A pdb=" N VAL J 176 " --> pdb=" O PHE J 172 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU J 190 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU J 191 " --> pdb=" O PHE J 187 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE J 192 " --> pdb=" O GLY J 188 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS J 203 " --> pdb=" O VAL J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 251 removed outlier: 3.965A pdb=" N GLN J 229 " --> pdb=" O ALA J 225 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN J 245 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN J 246 " --> pdb=" O LEU J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 267 removed outlier: 3.878A pdb=" N ILE J 264 " --> pdb=" O ASP J 260 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA J 265 " --> pdb=" O GLU J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 281 removed outlier: 3.584A pdb=" N TRP J 278 " --> pdb=" O PRO J 274 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE J 281 " --> pdb=" O GLN J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 303 removed outlier: 3.581A pdb=" N TRP J 302 " --> pdb=" O ARG J 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 15 removed outlier: 3.802A pdb=" N ASN K 15 " --> pdb=" O SER K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 35 removed outlier: 4.058A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU K 26 " --> pdb=" O LEU K 22 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU K 33 " --> pdb=" O GLY K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 removed outlier: 3.516A pdb=" N PHE K 55 " --> pdb=" O TYR K 51 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL K 57 " --> pdb=" O SER K 53 " (cutoff:3.500A) Proline residue: K 59 - end of helix removed outlier: 4.239A pdb=" N LEU K 63 " --> pdb=" O PRO K 59 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 82 removed outlier: 3.815A pdb=" N THR K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 112 Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.715A pdb=" N LEU K 116 " --> pdb=" O VAL K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 131 removed outlier: 3.599A pdb=" N GLU K 130 " --> pdb=" O GLY K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 158 Processing helix chain 'K' and resid 170 through 210 removed outlier: 3.794A pdb=" N TRP K 190 " --> pdb=" O GLN K 186 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE K 191 " --> pdb=" O MET K 187 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU K 192 " --> pdb=" O LEU K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 252 removed outlier: 3.624A pdb=" N TYR K 220 " --> pdb=" O LEU K 216 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG K 229 " --> pdb=" O LEU K 225 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU K 230 " --> pdb=" O GLN K 226 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE K 232 " --> pdb=" O GLU K 228 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET K 244 " --> pdb=" O SER K 240 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL L 5 " --> pdb=" O ALA L 23 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA L 23 " --> pdb=" O VAL L 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.883A pdb=" N VAL L 12 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA L 50 " --> pdb=" O HIS L 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 288 through 290 removed outlier: 4.218A pdb=" N ARG D 288 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AA5, first strand: chain 'H' and resid 289 through 290 Processing sheet with id=AA6, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AA7, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.650A pdb=" N VAL M 5 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.734A pdb=" N VAL M 93 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) 1553 hydrogen bonds defined for protein. 4584 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: 4.43 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6763 1.33 - 1.45: 4653 1.45 - 1.57: 13512 1.57 - 1.70: 0 1.70 - 1.82: 148 Bond restraints: 25076 Sorted by residual: bond pdb=" N ASP A 169 " pdb=" CA ASP A 169 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.48e+00 bond pdb=" N ASP B 169 " pdb=" CA ASP B 169 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.42e+00 bond pdb=" N TYR I 285 " pdb=" CA TYR I 285 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.16e-02 7.43e+03 7.14e+00 bond pdb=" N LYS L 76 " pdb=" CA LYS L 76 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 6.97e+00 bond pdb=" N ARG E 144 " pdb=" CA ARG E 144 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.25e-02 6.40e+03 6.87e+00 ... (remaining 25071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 33679 2.12 - 4.25: 325 4.25 - 6.37: 92 6.37 - 8.49: 13 8.49 - 10.62: 6 Bond angle restraints: 34115 Sorted by residual: angle pdb=" CB LYS G 258 " pdb=" CG LYS G 258 " pdb=" CD LYS G 258 " ideal model delta sigma weight residual 111.30 121.92 -10.62 2.30e+00 1.89e-01 2.13e+01 angle pdb=" N ARG E 181 " pdb=" CA ARG E 181 " pdb=" C ARG E 181 " ideal model delta sigma weight residual 111.07 107.07 4.00 1.07e+00 8.73e-01 1.40e+01 angle pdb=" N GLY F 305 " pdb=" CA GLY F 305 " pdb=" C GLY F 305 " ideal model delta sigma weight residual 115.27 110.26 5.01 1.41e+00 5.03e-01 1.26e+01 angle pdb=" C TYR E 285 " pdb=" CA TYR E 285 " pdb=" CB TYR E 285 " ideal model delta sigma weight residual 109.70 103.61 6.09 1.81e+00 3.05e-01 1.13e+01 angle pdb=" CB MET K 74 " pdb=" CG MET K 74 " pdb=" SD MET K 74 " ideal model delta sigma weight residual 112.70 122.59 -9.89 3.00e+00 1.11e-01 1.09e+01 ... (remaining 34110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 13115 17.73 - 35.47: 1367 35.47 - 53.20: 310 53.20 - 70.94: 34 70.94 - 88.67: 11 Dihedral angle restraints: 14837 sinusoidal: 5782 harmonic: 9055 Sorted by residual: dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 130 " pdb=" CB CYS C 130 " ideal model delta sinusoidal sigma weight residual -86.00 -167.67 81.67 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CA MET K 144 " pdb=" C MET K 144 " pdb=" N PHE K 145 " pdb=" CA PHE K 145 " ideal model delta harmonic sigma weight residual 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CB CYS C 48 " pdb=" SG CYS C 48 " pdb=" SG CYS C 162 " pdb=" CB CYS C 162 " ideal model delta sinusoidal sigma weight residual 93.00 126.20 -33.20 1 1.00e+01 1.00e-02 1.57e+01 ... (remaining 14834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2991 0.044 - 0.088: 695 0.088 - 0.132: 121 0.132 - 0.176: 9 0.176 - 0.220: 2 Chirality restraints: 3818 Sorted by residual: chirality pdb=" CA TYR E 285 " pdb=" N TYR E 285 " pdb=" C TYR E 285 " pdb=" CB TYR E 285 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TYR I 285 " pdb=" N TYR I 285 " pdb=" C TYR I 285 " pdb=" CB TYR I 285 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA ARG E 181 " pdb=" N ARG E 181 " pdb=" C ARG E 181 " pdb=" CB ARG E 181 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 3815 not shown) Planarity restraints: 4341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 182 " -0.012 2.00e-02 2.50e+03 1.40e-02 3.93e+00 pdb=" CG TYR E 182 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR E 182 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR E 182 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR E 182 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 182 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 182 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 182 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 304 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.78e+00 pdb=" C GLN F 304 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN F 304 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY F 305 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 172 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" C LEU B 172 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 172 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL B 173 " 0.011 2.00e-02 2.50e+03 ... (remaining 4338 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2614 2.74 - 3.28: 26238 3.28 - 3.82: 41273 3.82 - 4.36: 45766 4.36 - 4.90: 77051 Nonbonded interactions: 192942 Sorted by model distance: nonbonded pdb=" OH TYR D 285 " pdb=" O LEU D 295 " model vdw 2.198 3.040 nonbonded pdb=" CE2 PHE C 100 " pdb=" CG LYS C 206 " model vdw 2.204 3.740 nonbonded pdb=" O ASP B 169 " pdb=" OD1 ASP B 169 " model vdw 2.225 3.040 nonbonded pdb=" O ASP A 169 " pdb=" OD1 ASP A 169 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR C 182 " pdb=" O ARG D 52 " model vdw 2.230 3.040 ... (remaining 192937 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 5 through 255) selection = (chain 'B' and resid 5 through 255) selection = chain 'K' } ncs_group { reference = (chain 'C' and resid 38 through 305) selection = (chain 'D' and (resid 38 through 143 or (resid 144 through 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 147 through 162 or (resid 163 t \ hrough 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ or (resid 167 through 168 and (name N or name CA or name C or name O or name CB \ )) or resid 169 through 256 or (resid 257 through 262 and (name N or name CA or \ name C or name O or name CB )) or resid 263 through 305)) selection = (chain 'E' and (resid 38 through 143 or (resid 144 through 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 147 through 162 or (resid 163 t \ hrough 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ or (resid 167 through 168 and (name N or name CA or name C or name O or name CB \ )) or resid 169 through 256 or (resid 257 through 262 and (name N or name CA or \ name C or name O or name CB )) or resid 263 through 305)) selection = (chain 'F' and (resid 38 through 143 or (resid 144 through 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 147 through 162 or (resid 163 t \ hrough 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ or (resid 167 through 168 and (name N or name CA or name C or name O or name CB \ )) or resid 169 through 256 or (resid 257 through 262 and (name N or name CA or \ name C or name O or name CB )) or resid 263 through 305)) selection = (chain 'G' and (resid 38 through 143 or (resid 144 through 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 147 through 162 or (resid 163 t \ hrough 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ or (resid 167 through 168 and (name N or name CA or name C or name O or name CB \ )) or resid 169 through 256 or (resid 257 through 262 and (name N or name CA or \ name C or name O or name CB )) or resid 263 through 305)) selection = (chain 'H' and (resid 38 through 143 or (resid 144 through 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 147 through 162 or (resid 163 t \ hrough 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ or (resid 167 through 168 and (name N or name CA or name C or name O or name CB \ )) or resid 169 through 256 or (resid 257 through 262 and (name N or name CA or \ name C or name O or name CB )) or resid 263 through 305)) selection = (chain 'I' and (resid 38 through 143 or (resid 144 through 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 147 through 162 or (resid 163 t \ hrough 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ or (resid 167 through 168 and (name N or name CA or name C or name O or name CB \ )) or resid 169 through 256 or (resid 257 through 262 and (name N or name CA or \ name C or name O or name CB )) or resid 263 through 305)) } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.620 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.004 0.045 25097 Z= 0.185 Angle : 0.596 10.616 34157 Z= 0.314 Chirality : 0.038 0.220 3818 Planarity : 0.004 0.071 4341 Dihedral : 14.768 88.673 8906 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.46 % Allowed : 20.12 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.77 (0.16), residues: 3034 helix: 1.18 (0.12), residues: 1981 sheet: 0.58 (0.58), residues: 74 loop : -0.79 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 45 TYR 0.034 0.002 TYR E 182 PHE 0.022 0.001 PHE K 145 TRP 0.011 0.001 TRP J 189 HIS 0.006 0.001 HIS K 141 Details of bonding type rmsd covalent geometry : bond 0.00381 (25076) covalent geometry : angle 0.59593 (34115) SS BOND : bond 0.00360 ( 21) SS BOND : angle 0.78606 ( 42) hydrogen bonds : bond 0.24442 ( 1553) hydrogen bonds : angle 7.66009 ( 4584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 MET cc_start: 0.8006 (mpp) cc_final: 0.7774 (mpp) REVERT: F 182 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7467 (t80) REVERT: H 152 HIS cc_start: 0.7247 (m-70) cc_final: 0.6881 (m90) REVERT: J 222 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8841 (mm-40) REVERT: K 144 MET cc_start: 0.4606 (ppp) cc_final: 0.3813 (ppp) REVERT: K 220 TYR cc_start: 0.8072 (t80) cc_final: 0.7631 (t80) outliers start: 12 outliers final: 3 residues processed: 205 average time/residue: 0.1564 time to fit residues: 52.8960 Evaluate side-chains 153 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 182 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.1980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS L 107 GLN B 44 GLN B 141 HIS C 266 ASN D 246 ASN G 165 ASN ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 ASN I 216 GLN ** I 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.128281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.094008 restraints weight = 72164.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.094076 restraints weight = 41262.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.093913 restraints weight = 28609.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.094195 restraints weight = 26655.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.094380 restraints weight = 24700.193| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25097 Z= 0.139 Angle : 0.579 10.256 34157 Z= 0.300 Chirality : 0.039 0.270 3818 Planarity : 0.004 0.057 4341 Dihedral : 4.060 37.443 3397 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.32 % Allowed : 18.23 % Favored : 78.45 % 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: 1.42 (0.15), residues: 3034 helix: 1.78 (0.11), residues: 2040 sheet: 0.13 (0.51), residues: 78 loop : -0.89 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 233 TYR 0.030 0.002 TYR A 220 PHE 0.023 0.001 PHE A 160 TRP 0.020 0.001 TRP K 190 HIS 0.008 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00282 (25076) covalent geometry : angle 0.57878 (34115) SS BOND : bond 0.00437 ( 21) SS BOND : angle 0.88409 ( 42) hydrogen bonds : bond 0.05227 ( 1553) hydrogen bonds : angle 4.65447 ( 4584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 198 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.8154 (m-10) cc_final: 0.7763 (m-80) REVERT: A 185 SER cc_start: 0.8913 (t) cc_final: 0.8541 (p) REVERT: A 187 MET cc_start: 0.7362 (mmp) cc_final: 0.7071 (mmm) REVERT: A 219 CYS cc_start: 0.9083 (m) cc_final: 0.8482 (p) REVERT: A 245 MET cc_start: 0.8798 (tpt) cc_final: 0.8392 (tmm) REVERT: B 141 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.7290 (t-90) REVERT: C 55 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8710 (tp) REVERT: C 71 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8226 (mt) REVERT: C 181 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8444 (ttp80) REVERT: C 187 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8426 (t80) REVERT: C 264 ILE cc_start: 0.8066 (pt) cc_final: 0.7819 (mt) REVERT: E 37 GLU cc_start: 0.5112 (tt0) cc_final: 0.4872 (tt0) REVERT: F 262 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7695 (tm-30) REVERT: G 291 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7851 (tm-30) REVERT: H 152 HIS cc_start: 0.7624 (m-70) cc_final: 0.7046 (m90) REVERT: H 228 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7602 (t0) REVERT: H 229 GLN cc_start: 0.8828 (tp40) cc_final: 0.8541 (tp40) REVERT: I 260 ASP cc_start: 0.8048 (m-30) cc_final: 0.7404 (m-30) REVERT: K 129 TYR cc_start: 0.7578 (t80) cc_final: 0.7347 (t80) REVERT: K 220 TYR cc_start: 0.8282 (t80) cc_final: 0.7937 (t80) REVERT: M 83 MET cc_start: 0.7644 (mmp) cc_final: 0.7415 (mmp) outliers start: 86 outliers final: 35 residues processed: 270 average time/residue: 0.1486 time to fit residues: 66.5145 Evaluate side-chains 199 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 45 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 251 PHE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain M residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 69 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 280 optimal weight: 20.0000 chunk 135 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 262 optimal weight: 8.9990 chunk 155 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 278 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 107 GLN D 300 HIS E 246 ASN F 88 HIS ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 GLN I 88 HIS ** I 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 207 HIS K 246 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.128718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.093918 restraints weight = 72197.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.094276 restraints weight = 42680.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.094566 restraints weight = 29032.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.095015 restraints weight = 26598.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.095178 restraints weight = 23023.939| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25097 Z= 0.122 Angle : 0.556 10.958 34157 Z= 0.280 Chirality : 0.037 0.260 3818 Planarity : 0.003 0.061 4341 Dihedral : 3.832 25.587 3390 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.43 % Allowed : 19.24 % Favored : 77.33 % 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: 1.56 (0.15), residues: 3034 helix: 1.88 (0.11), residues: 2053 sheet: 0.63 (0.50), residues: 88 loop : -0.95 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 240 TYR 0.027 0.001 TYR A 220 PHE 0.022 0.001 PHE A 160 TRP 0.019 0.001 TRP K 190 HIS 0.016 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00249 (25076) covalent geometry : angle 0.55450 (34115) SS BOND : bond 0.00387 ( 21) SS BOND : angle 1.43791 ( 42) hydrogen bonds : bond 0.04308 ( 1553) hydrogen bonds : angle 4.18438 ( 4584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 181 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: A 128 TYR cc_start: 0.8060 (m-10) cc_final: 0.7671 (m-10) REVERT: A 144 MET cc_start: 0.8033 (tmm) cc_final: 0.7722 (tmm) REVERT: A 185 SER cc_start: 0.8805 (t) cc_final: 0.8425 (p) REVERT: A 219 CYS cc_start: 0.8935 (m) cc_final: 0.8578 (p) REVERT: A 245 MET cc_start: 0.8722 (tpt) cc_final: 0.8001 (tmm) REVERT: B 144 MET cc_start: 0.7771 (mpp) cc_final: 0.7471 (mpp) REVERT: C 22 MET cc_start: 0.8467 (tpp) cc_final: 0.8017 (mmt) REVERT: C 55 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8661 (tp) REVERT: C 71 ILE cc_start: 0.8540 (pt) cc_final: 0.8329 (mt) REVERT: C 187 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8351 (t80) REVERT: D 45 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7439 (t-90) REVERT: E 37 GLU cc_start: 0.5025 (tt0) cc_final: 0.4766 (tt0) REVERT: F 262 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7654 (tm-30) REVERT: G 291 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7863 (tm-30) REVERT: H 152 HIS cc_start: 0.7611 (m-70) cc_final: 0.7072 (m90) REVERT: H 228 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7595 (t0) REVERT: H 229 GLN cc_start: 0.8668 (tp40) cc_final: 0.8454 (tp40) REVERT: I 262 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: J 200 PHE cc_start: 0.8320 (t80) cc_final: 0.8118 (t80) REVERT: J 256 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8312 (pp) REVERT: K 129 TYR cc_start: 0.7874 (t80) cc_final: 0.7410 (t80) REVERT: K 220 TYR cc_start: 0.8295 (t80) cc_final: 0.7977 (t80) REVERT: K 242 LEU cc_start: 0.8947 (pp) cc_final: 0.8431 (tp) outliers start: 89 outliers final: 48 residues processed: 260 average time/residue: 0.1494 time to fit residues: 65.4083 Evaluate side-chains 206 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 45 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 216 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 251 PHE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 260 ASP Chi-restraints excluded: chain I residue 262 GLU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain M residue 86 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 275 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 240 optimal weight: 3.9990 chunk 196 optimal weight: 0.4980 chunk 153 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN H 76 ASN H 168 ASN ** I 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.127559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.099478 restraints weight = 67645.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097364 restraints weight = 71858.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.098524 restraints weight = 62075.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.098931 restraints weight = 41282.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.099586 restraints weight = 38751.976| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25097 Z= 0.114 Angle : 0.547 8.951 34157 Z= 0.272 Chirality : 0.037 0.297 3818 Planarity : 0.004 0.088 4341 Dihedral : 3.778 29.971 3390 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.47 % Allowed : 19.55 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.70 (0.16), residues: 3034 helix: 2.05 (0.12), residues: 2033 sheet: 0.88 (0.53), residues: 78 loop : -0.98 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 173 TYR 0.018 0.001 TYR E 56 PHE 0.022 0.001 PHE A 18 TRP 0.022 0.001 TRP K 190 HIS 0.006 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00237 (25076) covalent geometry : angle 0.54585 (34115) SS BOND : bond 0.00367 ( 21) SS BOND : angle 1.01645 ( 42) hydrogen bonds : bond 0.03769 ( 1553) hydrogen bonds : angle 3.94046 ( 4584) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 164 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 50 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: A 55 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.6998 (m-80) REVERT: A 187 MET cc_start: 0.7252 (mmt) cc_final: 0.6744 (mmm) REVERT: C 181 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7712 (ttp80) REVERT: C 187 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7962 (t80) REVERT: D 45 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6573 (t-90) REVERT: E 37 GLU cc_start: 0.4398 (tt0) cc_final: 0.4186 (tt0) REVERT: E 287 TYR cc_start: 0.7887 (t80) cc_final: 0.7628 (t80) REVERT: G 217 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: H 228 ASP cc_start: 0.7523 (t0) cc_final: 0.7312 (t0) REVERT: I 262 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: J 256 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8288 (pp) REVERT: K 242 LEU cc_start: 0.8319 (pp) cc_final: 0.7580 (tp) outliers start: 90 outliers final: 59 residues processed: 247 average time/residue: 0.1486 time to fit residues: 61.7103 Evaluate side-chains 213 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 145 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 45 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 216 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 217 GLU Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 251 PHE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 262 GLU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 214 TYR Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 41 CYS Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 113 ILE Chi-restraints excluded: chain M residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 169 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 6 optimal weight: 0.0000 chunk 296 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 195 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** I 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.128576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.100929 restraints weight = 74490.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.097946 restraints weight = 65400.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.099218 restraints weight = 55292.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.099314 restraints weight = 38828.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099732 restraints weight = 37314.180| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25097 Z= 0.127 Angle : 0.554 9.447 34157 Z= 0.276 Chirality : 0.038 0.238 3818 Planarity : 0.003 0.073 4341 Dihedral : 3.743 26.598 3390 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.59 % Allowed : 19.89 % Favored : 76.52 % 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: 1.79 (0.16), residues: 3034 helix: 2.10 (0.12), residues: 2039 sheet: 0.90 (0.53), residues: 78 loop : -0.93 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 224 TYR 0.016 0.001 TYR E 56 PHE 0.020 0.001 PHE B 160 TRP 0.014 0.001 TRP K 190 HIS 0.005 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00277 (25076) covalent geometry : angle 0.55368 (34115) SS BOND : bond 0.00302 ( 21) SS BOND : angle 0.96955 ( 42) hydrogen bonds : bond 0.03631 ( 1553) hydrogen bonds : angle 3.87444 ( 4584) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 162 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 50 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7352 (m-80) REVERT: A 55 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7458 (t80) REVERT: A 128 TYR cc_start: 0.7638 (m-80) cc_final: 0.6651 (m-80) REVERT: B 74 MET cc_start: 0.7985 (tmm) cc_final: 0.7643 (tmm) REVERT: C 181 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7959 (ttp80) REVERT: C 187 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8170 (t80) REVERT: D 45 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.7058 (t-90) REVERT: E 37 GLU cc_start: 0.4774 (tt0) cc_final: 0.4573 (tt0) REVERT: G 291 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7765 (tm-30) REVERT: H 228 ASP cc_start: 0.7784 (t0) cc_final: 0.7533 (t0) REVERT: I 262 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: J 256 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8342 (pp) REVERT: K 129 TYR cc_start: 0.7499 (t80) cc_final: 0.7056 (t80) REVERT: K 242 LEU cc_start: 0.8687 (pp) cc_final: 0.8027 (tp) outliers start: 93 outliers final: 67 residues processed: 244 average time/residue: 0.1496 time to fit residues: 60.9014 Evaluate side-chains 225 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 150 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 45 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 251 PHE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 262 GLU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 41 CYS Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 186 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 300 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 246 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 128 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.129300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.101585 restraints weight = 74238.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099190 restraints weight = 52944.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.100092 restraints weight = 48785.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.100404 restraints weight = 32798.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.101990 restraints weight = 30732.373| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25097 Z= 0.111 Angle : 0.540 9.450 34157 Z= 0.268 Chirality : 0.037 0.232 3818 Planarity : 0.003 0.041 4341 Dihedral : 3.700 26.347 3390 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.43 % Allowed : 20.01 % Favored : 76.56 % 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: 1.88 (0.16), residues: 3034 helix: 2.17 (0.12), residues: 2041 sheet: 0.99 (0.53), residues: 78 loop : -0.91 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 173 TYR 0.013 0.001 TYR L 95 PHE 0.021 0.001 PHE B 160 TRP 0.016 0.001 TRP K 190 HIS 0.007 0.001 HIS J 207 Details of bonding type rmsd covalent geometry : bond 0.00232 (25076) covalent geometry : angle 0.53921 (34115) SS BOND : bond 0.00747 ( 21) SS BOND : angle 0.98836 ( 42) hydrogen bonds : bond 0.03462 ( 1553) hydrogen bonds : angle 3.75017 ( 4584) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 171 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8256 (mp) REVERT: A 50 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: A 55 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7434 (t80) REVERT: A 128 TYR cc_start: 0.7685 (m-80) cc_final: 0.6620 (m-80) REVERT: B 214 THR cc_start: 0.7186 (OUTLIER) cc_final: 0.6962 (p) REVERT: C 187 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8176 (t80) REVERT: E 37 GLU cc_start: 0.4687 (tt0) cc_final: 0.4458 (tt0) REVERT: H 190 LEU cc_start: 0.8549 (mm) cc_final: 0.8325 (mm) REVERT: H 228 ASP cc_start: 0.7780 (t0) cc_final: 0.7530 (t0) REVERT: I 262 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: J 187 PHE cc_start: 0.7611 (m-80) cc_final: 0.6767 (m-80) REVERT: J 256 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8339 (pp) REVERT: K 129 TYR cc_start: 0.7587 (t80) cc_final: 0.7187 (t80) REVERT: K 242 LEU cc_start: 0.8624 (pp) cc_final: 0.7935 (tp) outliers start: 89 outliers final: 62 residues processed: 249 average time/residue: 0.1577 time to fit residues: 64.4232 Evaluate side-chains 227 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 158 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 216 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 262 GLU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 86 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 230 optimal weight: 0.0000 chunk 224 optimal weight: 0.9980 chunk 270 optimal weight: 0.9990 chunk 34 optimal weight: 40.0000 chunk 85 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.127651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.100636 restraints weight = 74271.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.098530 restraints weight = 69561.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.099550 restraints weight = 59292.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.100040 restraints weight = 39019.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.100212 restraints weight = 36990.075| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25097 Z= 0.153 Angle : 0.572 12.561 34157 Z= 0.286 Chirality : 0.038 0.227 3818 Planarity : 0.003 0.039 4341 Dihedral : 3.733 24.405 3390 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.82 % Allowed : 19.66 % Favored : 76.52 % 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: 1.86 (0.16), residues: 3034 helix: 2.17 (0.12), residues: 2036 sheet: 1.01 (0.53), residues: 78 loop : -0.92 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 173 TYR 0.027 0.001 TYR A 220 PHE 0.019 0.001 PHE B 160 TRP 0.033 0.001 TRP K 118 HIS 0.005 0.001 HIS J 207 Details of bonding type rmsd covalent geometry : bond 0.00340 (25076) covalent geometry : angle 0.57098 (34115) SS BOND : bond 0.00335 ( 21) SS BOND : angle 0.91296 ( 42) hydrogen bonds : bond 0.03526 ( 1553) hydrogen bonds : angle 3.78752 ( 4584) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 158 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8275 (mp) REVERT: A 50 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: A 55 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.6993 (t80) REVERT: A 128 TYR cc_start: 0.7585 (m-80) cc_final: 0.6293 (m-10) REVERT: A 130 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6026 (tm-30) REVERT: B 74 MET cc_start: 0.8020 (tmm) cc_final: 0.7699 (tmm) REVERT: B 214 THR cc_start: 0.7088 (OUTLIER) cc_final: 0.6848 (p) REVERT: C 187 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8259 (t80) REVERT: E 203 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8302 (tptp) REVERT: G 291 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7883 (tm-30) REVERT: H 190 LEU cc_start: 0.8557 (mm) cc_final: 0.8344 (mm) REVERT: H 228 ASP cc_start: 0.7847 (t0) cc_final: 0.7593 (t0) REVERT: I 262 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: J 256 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8373 (pp) REVERT: K 129 TYR cc_start: 0.7593 (t80) cc_final: 0.7204 (t80) REVERT: K 249 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7834 (mmmm) REVERT: M 82 GLN cc_start: 0.7836 (tp40) cc_final: 0.7418 (tp40) outliers start: 99 outliers final: 76 residues processed: 245 average time/residue: 0.1481 time to fit residues: 60.7315 Evaluate side-chains 236 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 150 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 216 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 262 GLU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 220 TRP Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 249 LYS Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 86 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 44 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 276 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 294 optimal weight: 40.0000 chunk 103 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 24 optimal weight: 30.0000 chunk 266 optimal weight: 0.0980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.128955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.095200 restraints weight = 74350.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.094888 restraints weight = 42256.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.095335 restraints weight = 29163.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.095620 restraints weight = 26369.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.095685 restraints weight = 24134.064| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25097 Z= 0.111 Angle : 0.563 13.048 34157 Z= 0.277 Chirality : 0.037 0.216 3818 Planarity : 0.003 0.037 4341 Dihedral : 3.683 24.326 3390 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.43 % Allowed : 20.70 % Favored : 75.87 % 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: 1.96 (0.16), residues: 3034 helix: 2.24 (0.11), residues: 2047 sheet: 1.03 (0.54), residues: 78 loop : -0.93 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 224 TYR 0.028 0.001 TYR A 220 PHE 0.020 0.001 PHE B 160 TRP 0.028 0.001 TRP K 118 HIS 0.005 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00235 (25076) covalent geometry : angle 0.56256 (34115) SS BOND : bond 0.00359 ( 21) SS BOND : angle 1.04264 ( 42) hydrogen bonds : bond 0.03360 ( 1553) hydrogen bonds : angle 3.67135 ( 4584) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 164 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 50 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7744 (m-10) REVERT: A 55 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 128 TYR cc_start: 0.7769 (m-80) cc_final: 0.6350 (m-10) REVERT: A 227 ASN cc_start: 0.8409 (m-40) cc_final: 0.8022 (t0) REVERT: A 244 MET cc_start: 0.6768 (mtp) cc_final: 0.6554 (mtp) REVERT: B 74 MET cc_start: 0.8002 (tmm) cc_final: 0.7748 (tmm) REVERT: B 214 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.7100 (p) REVERT: C 187 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8332 (t80) REVERT: D 45 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.6746 (t-90) REVERT: E 203 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8157 (tptp) REVERT: G 291 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7656 (tm-30) REVERT: H 204 CYS cc_start: 0.8962 (p) cc_final: 0.8564 (p) REVERT: H 228 ASP cc_start: 0.7826 (t0) cc_final: 0.7596 (t0) REVERT: I 58 LEU cc_start: 0.8530 (tt) cc_final: 0.8237 (mm) REVERT: I 262 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: J 187 PHE cc_start: 0.7693 (m-80) cc_final: 0.6855 (m-80) REVERT: J 256 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8361 (pp) REVERT: K 129 TYR cc_start: 0.7916 (t80) cc_final: 0.7614 (t80) REVERT: K 181 HIS cc_start: 0.8128 (m90) cc_final: 0.7134 (m-70) REVERT: K 246 HIS cc_start: 0.7801 (t-90) cc_final: 0.7289 (t70) REVERT: K 249 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7836 (mmmm) outliers start: 89 outliers final: 70 residues processed: 243 average time/residue: 0.1468 time to fit residues: 59.9386 Evaluate side-chains 230 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 150 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 45 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 216 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 251 PHE Chi-restraints excluded: chain I residue 262 GLU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 220 TRP Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 249 LYS Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 86 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 48 optimal weight: 0.5980 chunk 171 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.128896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.101393 restraints weight = 74684.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.099159 restraints weight = 52941.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099934 restraints weight = 49316.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.100265 restraints weight = 32954.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.101803 restraints weight = 30671.880| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25097 Z= 0.114 Angle : 0.565 11.747 34157 Z= 0.277 Chirality : 0.038 0.262 3818 Planarity : 0.003 0.037 4341 Dihedral : 3.651 24.057 3390 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.35 % Allowed : 20.78 % Favored : 75.87 % 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: 2.02 (0.16), residues: 3034 helix: 2.32 (0.11), residues: 2035 sheet: 1.00 (0.50), residues: 92 loop : -0.96 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 224 TYR 0.027 0.001 TYR A 220 PHE 0.020 0.001 PHE B 160 TRP 0.027 0.001 TRP K 118 HIS 0.005 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00247 (25076) covalent geometry : angle 0.56310 (34115) SS BOND : bond 0.00318 ( 21) SS BOND : angle 1.27981 ( 42) hydrogen bonds : bond 0.03295 ( 1553) hydrogen bonds : angle 3.63100 ( 4584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 154 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8372 (mp) REVERT: A 55 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7255 (t80) REVERT: A 128 TYR cc_start: 0.7555 (m-80) cc_final: 0.6495 (m-80) REVERT: A 227 ASN cc_start: 0.8281 (m-40) cc_final: 0.8026 (t0) REVERT: B 74 MET cc_start: 0.7973 (tmm) cc_final: 0.7661 (tmm) REVERT: B 214 THR cc_start: 0.7207 (OUTLIER) cc_final: 0.7005 (p) REVERT: C 187 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8217 (t80) REVERT: D 45 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6688 (t-90) REVERT: E 203 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8313 (tptp) REVERT: H 204 CYS cc_start: 0.8854 (p) cc_final: 0.8540 (p) REVERT: H 228 ASP cc_start: 0.7816 (t0) cc_final: 0.7565 (t0) REVERT: H 259 ASP cc_start: 0.7687 (p0) cc_final: 0.7132 (p0) REVERT: I 58 LEU cc_start: 0.8508 (tt) cc_final: 0.8238 (mm) REVERT: I 262 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: J 256 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8357 (pp) REVERT: K 129 TYR cc_start: 0.7790 (t80) cc_final: 0.7493 (t80) REVERT: K 181 HIS cc_start: 0.7953 (m90) cc_final: 0.6965 (m-70) REVERT: K 246 HIS cc_start: 0.7625 (t-90) cc_final: 0.7188 (t70) REVERT: K 249 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7820 (mmmm) outliers start: 87 outliers final: 72 residues processed: 230 average time/residue: 0.1518 time to fit residues: 58.0313 Evaluate side-chains 229 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 148 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 45 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 216 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 226 ASN Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 251 PHE Chi-restraints excluded: chain I residue 262 GLU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 220 TRP Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 249 LYS Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 198 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 225 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 139 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.129436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.096018 restraints weight = 74376.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.095755 restraints weight = 42408.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.096166 restraints weight = 29462.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.096422 restraints weight = 28573.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.096491 restraints weight = 24194.242| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25097 Z= 0.107 Angle : 0.564 11.523 34157 Z= 0.275 Chirality : 0.037 0.203 3818 Planarity : 0.003 0.036 4341 Dihedral : 3.617 24.548 3390 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.05 % Allowed : 21.09 % Favored : 75.87 % 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: 2.10 (0.16), residues: 3034 helix: 2.36 (0.11), residues: 2047 sheet: 1.04 (0.51), residues: 92 loop : -0.93 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 38 TYR 0.028 0.001 TYR A 220 PHE 0.019 0.001 PHE F 267 TRP 0.027 0.001 TRP K 118 HIS 0.005 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00227 (25076) covalent geometry : angle 0.56262 (34115) SS BOND : bond 0.00359 ( 21) SS BOND : angle 1.21808 ( 42) hydrogen bonds : bond 0.03216 ( 1553) hydrogen bonds : angle 3.56071 ( 4584) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 161 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 50 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 55 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.6960 (t80) REVERT: A 128 TYR cc_start: 0.7431 (m-80) cc_final: 0.6289 (m-80) REVERT: A 227 ASN cc_start: 0.8334 (m-40) cc_final: 0.8075 (t0) REVERT: C 187 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8291 (t80) REVERT: D 45 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.6816 (t-90) REVERT: E 203 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8259 (tptp) REVERT: H 204 CYS cc_start: 0.8975 (p) cc_final: 0.8616 (p) REVERT: H 228 ASP cc_start: 0.7833 (t0) cc_final: 0.7601 (t0) REVERT: H 259 ASP cc_start: 0.7831 (p0) cc_final: 0.7254 (p0) REVERT: I 58 LEU cc_start: 0.8552 (tt) cc_final: 0.8280 (mm) REVERT: I 262 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: J 256 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8348 (pp) REVERT: K 129 TYR cc_start: 0.7997 (t80) cc_final: 0.7633 (t80) REVERT: K 181 HIS cc_start: 0.8253 (m90) cc_final: 0.7280 (m-70) REVERT: K 190 TRP cc_start: 0.8278 (m-90) cc_final: 0.7794 (m-90) REVERT: K 246 HIS cc_start: 0.7844 (t-90) cc_final: 0.7284 (t-170) REVERT: M 83 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6804 (mmp) REVERT: M 94 TYR cc_start: 0.8327 (m-10) cc_final: 0.8009 (m-10) outliers start: 79 outliers final: 66 residues processed: 230 average time/residue: 0.1521 time to fit residues: 58.7843 Evaluate side-chains 225 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 150 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 224 HIS Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 226 ASN Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 45 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 216 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 251 PHE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 251 PHE Chi-restraints excluded: chain I residue 262 GLU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 220 TRP Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 268 optimal weight: 40.0000 chunk 81 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 295 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.127341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.100076 restraints weight = 74522.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.097669 restraints weight = 67403.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.098813 restraints weight = 58710.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.099059 restraints weight = 39423.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099329 restraints weight = 38286.865| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25097 Z= 0.162 Angle : 0.597 11.287 34157 Z= 0.297 Chirality : 0.039 0.198 3818 Planarity : 0.003 0.035 4341 Dihedral : 3.721 22.153 3390 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.28 % Allowed : 21.05 % Favored : 75.67 % 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: 2.01 (0.16), residues: 3034 helix: 2.30 (0.11), residues: 2036 sheet: 0.97 (0.50), residues: 92 loop : -0.96 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 38 TYR 0.035 0.002 TYR F 285 PHE 0.019 0.001 PHE B 160 TRP 0.027 0.001 TRP K 118 HIS 0.005 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00365 (25076) covalent geometry : angle 0.59569 (34115) SS BOND : bond 0.00358 ( 21) SS BOND : angle 1.14408 ( 42) hydrogen bonds : bond 0.03436 ( 1553) hydrogen bonds : angle 3.68876 ( 4584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.36 seconds wall clock time: 66 minutes 57.53 seconds (4017.53 seconds total)