Starting phenix.real_space_refine on Fri May 23 15:55:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rml_19363/05_2025/8rml_19363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rml_19363/05_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_19363/05_2025/8rml_19363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rml_19363/05_2025/8rml_19363.map" model { file = "/net/cci-nas-00/data/ceres_data/8rml_19363/05_2025/8rml_19363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rml_19363/05_2025/8rml_19363.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 5, 'ARG:plan': 1, '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, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} 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: 14.52, per 1000 atoms: 0.59 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: 6.24 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 2.59 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: 7.15 Time building geometry restraints manager: 7.30 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: 1.230 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: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 52.110 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.110 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.700 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (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 TRP 0.011 0.001 TRP J 189 HIS 0.006 0.001 HIS K 141 PHE 0.022 0.001 PHE K 145 TYR 0.034 0.002 TYR E 182 ARG 0.005 0.000 ARG M 45 Details of bonding type rmsd hydrogen bonds : bond 0.24442 ( 1553) hydrogen bonds : angle 7.66009 ( 4584) SS BOND : bond 0.00360 ( 21) SS BOND : angle 0.78606 ( 42) covalent geometry : bond 0.00381 (25076) covalent geometry : angle 0.59593 (34115) *********************** 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 : 2.788 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: B 144 MET cc_start: 0.8006 (mpp) cc_final: 0.7773 (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: 0.6879 (m90) REVERT: K 144 MET cc_start: 0.4606 (ppp) cc_final: 0.3810 (ppp) REVERT: K 220 TYR cc_start: 0.8072 (t80) cc_final: 0.7630 (t80) outliers start: 12 outliers final: 4 residues processed: 205 average time/residue: 0.3219 time to fit residues: 108.5608 Evaluate side-chains 154 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 76 LYS 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 255 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 237 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 216 GLN C 266 ASN D 246 ASN D 300 HIS E 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.128880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.094819 restraints weight = 72143.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.094842 restraints weight = 40727.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.094956 restraints weight = 27645.001| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1664 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= 0.132 Angle : 0.572 9.539 34157 Z= 0.296 Chirality : 0.038 0.267 3818 Planarity : 0.004 0.055 4341 Dihedral : 4.058 37.056 3401 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.39 % Allowed : 18.12 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.15), residues: 3034 helix: 1.80 (0.11), residues: 2043 sheet: 0.13 (0.51), residues: 78 loop : -0.88 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 190 HIS 0.010 0.001 HIS A 218 PHE 0.023 0.001 PHE A 160 TYR 0.028 0.002 TYR A 220 ARG 0.004 0.000 ARG L 35 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 1553) hydrogen bonds : angle 4.58678 ( 4584) SS BOND : bond 0.00436 ( 21) SS BOND : angle 0.85973 ( 42) covalent geometry : bond 0.00260 (25076) covalent geometry : angle 0.57147 (34115) *********************** 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 286 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 198 time to evaluate : 2.765 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 128 TYR cc_start: 0.7988 (m-10) cc_final: 0.7634 (m-80) REVERT: A 185 SER cc_start: 0.8865 (t) cc_final: 0.8492 (p) REVERT: A 187 MET cc_start: 0.7509 (mmp) cc_final: 0.7302 (mmm) REVERT: A 245 MET cc_start: 0.8723 (tpt) cc_final: 0.8368 (tmm) REVERT: C 55 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8732 (tp) REVERT: C 71 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8200 (mt) REVERT: C 181 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8493 (ttp80) REVERT: C 187 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8371 (t80) REVERT: C 264 ILE cc_start: 0.8022 (pt) cc_final: 0.7767 (mt) REVERT: D 163 LYS cc_start: 0.7474 (tppt) cc_final: 0.6041 (tppt) REVERT: E 37 GLU cc_start: 0.5075 (tt0) cc_final: 0.4840 (tt0) REVERT: E 137 ASP cc_start: 0.7525 (t0) cc_final: 0.7310 (t0) REVERT: F 262 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7671 (tm-30) REVERT: G 291 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7765 (tm-30) REVERT: H 152 HIS cc_start: 0.7604 (m-70) cc_final: 0.7024 (m90) REVERT: H 228 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7561 (t0) REVERT: H 229 GLN cc_start: 0.8826 (tp40) cc_final: 0.8539 (tp40) REVERT: I 260 ASP cc_start: 0.8024 (m-30) cc_final: 0.7370 (m-30) REVERT: K 129 TYR cc_start: 0.7557 (t80) cc_final: 0.7320 (t80) REVERT: K 220 TYR cc_start: 0.8290 (t80) cc_final: 0.7974 (t80) REVERT: M 83 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7358 (mmp) outliers start: 88 outliers final: 33 residues processed: 272 average time/residue: 0.3084 time to fit residues: 138.9080 Evaluate side-chains 195 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 2.746 ------------------------------------------------------------------------------- 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 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 182 TYR 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 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 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 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 83 MET 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 82 optimal weight: 6.9990 chunk 222 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 230 optimal weight: 10.0000 chunk 228 optimal weight: 0.0070 chunk 202 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 197 optimal weight: 0.0370 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 107 GLN B 44 GLN C 216 GLN F 88 HIS G 226 ASN ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.128437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099986 restraints weight = 71916.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.097110 restraints weight = 48746.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.097927 restraints weight = 46477.783| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25097 Z= 0.130 Angle : 0.561 11.269 34157 Z= 0.283 Chirality : 0.038 0.292 3818 Planarity : 0.003 0.061 4341 Dihedral : 3.835 25.584 3390 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.62 % Allowed : 19.08 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.15), residues: 3034 helix: 1.87 (0.11), residues: 2052 sheet: 0.66 (0.50), residues: 88 loop : -0.92 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 190 HIS 0.012 0.001 HIS A 141 PHE 0.022 0.001 PHE B 160 TYR 0.021 0.001 TYR A 220 ARG 0.005 0.000 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 1553) hydrogen bonds : angle 4.22112 ( 4584) SS BOND : bond 0.00400 ( 21) SS BOND : angle 1.36203 ( 42) covalent geometry : bond 0.00274 (25076) covalent geometry : angle 0.55901 (34115) *********************** 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 266 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 172 time to evaluate : 2.651 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 50 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: A 128 TYR cc_start: 0.7914 (m-10) cc_final: 0.7613 (m-10) REVERT: A 144 MET cc_start: 0.7978 (tmm) cc_final: 0.7700 (tmm) REVERT: A 185 SER cc_start: 0.8742 (t) cc_final: 0.8397 (p) REVERT: A 187 MET cc_start: 0.7370 (mmp) cc_final: 0.7143 (mmm) REVERT: A 219 CYS cc_start: 0.8810 (m) cc_final: 0.8474 (p) REVERT: A 245 MET cc_start: 0.8555 (tpt) cc_final: 0.7915 (tmm) REVERT: B 144 MET cc_start: 0.7657 (mpp) cc_final: 0.7308 (mpp) REVERT: C 22 MET cc_start: 0.8556 (tpp) cc_final: 0.8119 (mmt) REVERT: C 55 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8739 (tp) REVERT: C 71 ILE cc_start: 0.8559 (pt) cc_final: 0.8321 (mt) REVERT: C 181 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7292 (ttp80) REVERT: C 187 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8259 (t80) REVERT: D 45 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.6490 (t-90) REVERT: E 37 GLU cc_start: 0.5056 (tt0) cc_final: 0.4823 (tt0) REVERT: E 137 ASP cc_start: 0.7432 (t0) cc_final: 0.7221 (t0) REVERT: F 262 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7764 (tm-30) REVERT: G 291 GLN cc_start: 0.8235 (tm-30) cc_final: 0.8011 (tm-30) REVERT: H 152 HIS cc_start: 0.7557 (m-70) cc_final: 0.7006 (m90) REVERT: H 228 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7587 (t0) REVERT: I 262 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: J 256 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8316 (pp) REVERT: K 129 TYR cc_start: 0.7741 (t80) cc_final: 0.7355 (t80) REVERT: K 220 TYR cc_start: 0.8349 (t80) cc_final: 0.8068 (t80) REVERT: K 242 LEU cc_start: 0.8861 (pp) cc_final: 0.8277 (tp) outliers start: 94 outliers final: 54 residues processed: 257 average time/residue: 0.2905 time to fit residues: 124.5681 Evaluate side-chains 213 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 151 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 127 THR 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 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 181 ARG 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 61 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 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 119 VAL Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 204 CYS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 106 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 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 217 GLU Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 68 PHE 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 32 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 269 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 243 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 262 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS ** D 277 GLN ** 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** J 207 HIS K 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.127281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.099076 restraints weight = 67787.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096617 restraints weight = 69028.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.097824 restraints weight = 59602.703| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25097 Z= 0.112 Angle : 0.539 11.003 34157 Z= 0.267 Chirality : 0.037 0.286 3818 Planarity : 0.003 0.052 4341 Dihedral : 3.762 27.607 3390 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.32 % Allowed : 19.78 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.16), residues: 3034 helix: 2.05 (0.11), residues: 2035 sheet: 0.89 (0.53), residues: 78 loop : -0.93 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 190 HIS 0.004 0.001 HIS J 238 PHE 0.023 0.001 PHE A 18 TYR 0.019 0.001 TYR E 56 ARG 0.005 0.000 ARG I 144 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 1553) hydrogen bonds : angle 3.94685 ( 4584) SS BOND : bond 0.00272 ( 21) SS BOND : angle 0.85170 ( 42) covalent geometry : bond 0.00230 (25076) covalent geometry : angle 0.53816 (34115) *********************** 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 257 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 171 time to evaluate : 2.672 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: A 22 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8365 (mp) REVERT: A 50 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7146 (m-10) REVERT: C 187 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.8002 (t80) REVERT: E 37 GLU cc_start: 0.4486 (tt0) cc_final: 0.4257 (tt0) REVERT: E 287 TYR cc_start: 0.7891 (t80) cc_final: 0.7630 (t80) REVERT: I 262 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: J 256 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8265 (pp) REVERT: K 242 LEU cc_start: 0.8346 (pp) cc_final: 0.7620 (tp) outliers start: 86 outliers final: 53 residues processed: 250 average time/residue: 0.2980 time to fit residues: 125.0854 Evaluate side-chains 204 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 41 CYS Chi-restraints excluded: chain A residue 50 TYR 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 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 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 E residue 119 VAL Chi-restraints excluded: chain E residue 192 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 F residue 239 SER Chi-restraints excluded: chain F residue 282 THR 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 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 68 PHE Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 170 VAL 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 204 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 299 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 270 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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** I 88 HIS ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 HIS M 59 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 = 0.129308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.101820 restraints weight = 74814.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.099784 restraints weight = 52840.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.100684 restraints weight = 46418.979| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25097 Z= 0.108 Angle : 0.541 10.126 34157 Z= 0.268 Chirality : 0.037 0.236 3818 Planarity : 0.003 0.048 4341 Dihedral : 3.694 25.697 3390 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.93 % Allowed : 20.16 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.16), residues: 3034 helix: 2.14 (0.12), residues: 2039 sheet: 1.00 (0.53), residues: 78 loop : -0.93 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 190 HIS 0.018 0.001 HIS I 88 PHE 0.023 0.001 PHE K 39 TYR 0.025 0.001 TYR A 220 ARG 0.004 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 1553) hydrogen bonds : angle 3.81250 ( 4584) SS BOND : bond 0.00619 ( 21) SS BOND : angle 0.89521 ( 42) covalent geometry : bond 0.00221 (25076) covalent geometry : angle 0.54085 (34115) *********************** 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 243 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 167 time to evaluate : 2.823 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: 0.8225 (mp) REVERT: A 50 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: A 187 MET cc_start: 0.7594 (mmm) cc_final: 0.7297 (mmm) REVERT: B 74 MET cc_start: 0.8003 (tmm) cc_final: 0.7679 (tmm) REVERT: B 214 THR cc_start: 0.7124 (OUTLIER) cc_final: 0.6897 (p) REVERT: C 187 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8215 (t80) REVERT: D 45 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.6888 (t-90) REVERT: D 258 LYS cc_start: 0.8661 (ptpp) cc_final: 0.8303 (pttm) REVERT: E 37 GLU cc_start: 0.4832 (tt0) cc_final: 0.4628 (tt0) REVERT: E 287 TYR cc_start: 0.7881 (t80) cc_final: 0.7590 (t80) REVERT: G 259 ASP cc_start: 0.8383 (p0) cc_final: 0.7467 (p0) REVERT: I 262 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: J 256 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8312 (pp) REVERT: K 181 HIS cc_start: 0.7825 (m90) cc_final: 0.7040 (m-70) REVERT: K 242 LEU cc_start: 0.8653 (pp) cc_final: 0.7984 (tp) REVERT: M 83 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7144 (mmp) outliers start: 76 outliers final: 50 residues processed: 235 average time/residue: 0.3113 time to fit residues: 124.7970 Evaluate side-chains 205 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 147 time to evaluate : 2.823 ------------------------------------------------------------------------------- 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 170 VAL Chi-restraints excluded: chain A residue 213 LEU 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 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 212 LEU 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 E residue 53 ASN Chi-restraints excluded: chain E residue 106 ILE 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 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 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 186 LEU 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 212 LEU Chi-restraints excluded: chain I residue 230 LEU 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 112 VAL Chi-restraints excluded: chain J residue 182 TYR Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 41 CYS Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain M residue 59 HIS 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 10 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 chunk 283 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 HIS M 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.128767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.101010 restraints weight = 74418.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098474 restraints weight = 52343.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.099377 restraints weight = 47755.933| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.003 0.030 25097 Z= 0.123 Angle : 0.548 9.552 34157 Z= 0.274 Chirality : 0.037 0.235 3818 Planarity : 0.003 0.045 4341 Dihedral : 3.674 24.951 3390 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.20 % Allowed : 20.47 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.16), residues: 3034 helix: 2.18 (0.12), residues: 2041 sheet: 1.05 (0.53), residues: 78 loop : -0.92 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 190 HIS 0.010 0.001 HIS M 59 PHE 0.022 0.001 PHE K 68 TYR 0.028 0.001 TYR A 220 ARG 0.004 0.000 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 1553) hydrogen bonds : angle 3.76900 ( 4584) SS BOND : bond 0.00283 ( 21) SS BOND : angle 0.82722 ( 42) covalent geometry : bond 0.00266 (25076) covalent geometry : angle 0.54735 (34115) *********************** 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 245 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 162 time to evaluate : 2.777 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: 0.8763 (OUTLIER) cc_final: 0.8243 (mp) REVERT: A 50 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: A 187 MET cc_start: 0.7678 (mmm) cc_final: 0.7344 (mmm) REVERT: B 214 THR cc_start: 0.7237 (OUTLIER) cc_final: 0.7005 (p) REVERT: C 181 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7467 (ttp80) REVERT: C 187 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8245 (t80) REVERT: D 45 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.6316 (t-90) REVERT: E 203 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8252 (tptp) REVERT: E 287 TYR cc_start: 0.7915 (t80) cc_final: 0.7671 (t80) REVERT: G 259 ASP cc_start: 0.8568 (p0) cc_final: 0.7609 (p0) REVERT: G 291 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7803 (tm-30) REVERT: H 190 LEU cc_start: 0.8586 (mm) cc_final: 0.8381 (mm) REVERT: I 258 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8392 (mmtt) REVERT: I 262 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: J 256 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8336 (pp) REVERT: K 56 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7651 (tt) REVERT: K 181 HIS cc_start: 0.7855 (m90) cc_final: 0.7122 (m-70) REVERT: K 242 LEU cc_start: 0.8658 (pp) cc_final: 0.7984 (tp) REVERT: M 83 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7135 (mmp) outliers start: 83 outliers final: 59 residues processed: 233 average time/residue: 0.3280 time to fit residues: 124.8365 Evaluate side-chains 220 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 149 time to evaluate : 2.789 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 213 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 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 181 ARG Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 212 LEU 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 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 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 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 G residue 71 ILE 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 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 220 TRP Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain K residue 41 CYS Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain M residue 59 HIS 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 220 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 265 optimal weight: 0.0070 chunk 121 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 28 optimal weight: 50.0000 chunk 272 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- 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** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 HIS ** 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 = 0.4163 r_free = 0.4163 target = 0.127851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.100894 restraints weight = 74630.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.098110 restraints weight = 65520.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.099299 restraints weight = 56822.880| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25097 Z= 0.144 Angle : 0.567 9.886 34157 Z= 0.285 Chirality : 0.038 0.228 3818 Planarity : 0.003 0.042 4341 Dihedral : 3.717 24.032 3390 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.70 % Allowed : 20.16 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.16), residues: 3034 helix: 2.14 (0.11), residues: 2054 sheet: 1.11 (0.53), residues: 78 loop : -0.96 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 190 HIS 0.014 0.001 HIS M 59 PHE 0.020 0.001 PHE B 160 TYR 0.030 0.001 TYR A 220 ARG 0.003 0.000 ARG K 103 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 1553) hydrogen bonds : angle 3.78433 ( 4584) SS BOND : bond 0.00298 ( 21) SS BOND : angle 0.93188 ( 42) covalent geometry : bond 0.00319 (25076) covalent geometry : angle 0.56691 (34115) *********************** 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 255 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 159 time to evaluate : 2.992 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: 0.8776 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 74 MET cc_start: 0.8022 (tmm) cc_final: 0.7774 (tmm) REVERT: B 214 THR cc_start: 0.7138 (OUTLIER) cc_final: 0.6917 (p) REVERT: C 181 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7531 (ttp80) REVERT: C 187 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8302 (t80) REVERT: D 45 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6354 (t-90) REVERT: E 203 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8271 (tptp) REVERT: G 291 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8012 (tm-30) REVERT: I 262 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: J 187 PHE cc_start: 0.7703 (m-80) cc_final: 0.6856 (m-80) REVERT: J 256 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8396 (pp) REVERT: K 181 HIS cc_start: 0.7838 (m90) cc_final: 0.7143 (m-70) REVERT: K 187 MET cc_start: 0.7724 (tmm) cc_final: 0.7435 (tmm) REVERT: K 249 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7774 (mmmt) REVERT: M 83 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7051 (mmp) outliers start: 96 outliers final: 68 residues processed: 245 average time/residue: 0.3122 time to fit residues: 125.8106 Evaluate side-chains 225 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 147 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 172 LEU 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 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 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 66 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 212 LEU 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 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 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 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 281 ILE 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 198 LEU Chi-restraints excluded: chain G residue 205 LEU 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 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 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 113 ILE 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 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 183 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 66 optimal weight: 0.0670 chunk 184 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 227 optimal weight: 30.0000 chunk 142 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 HIS M 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.128653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.101364 restraints weight = 74718.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.098547 restraints weight = 62534.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.099820 restraints weight = 53665.664| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25097 Z= 0.115 Angle : 0.570 13.033 34157 Z= 0.281 Chirality : 0.038 0.219 3818 Planarity : 0.003 0.040 4341 Dihedral : 3.698 24.441 3390 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.43 % Allowed : 20.66 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.16), residues: 3034 helix: 2.21 (0.11), residues: 2049 sheet: 1.11 (0.54), residues: 78 loop : -0.96 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP K 118 HIS 0.005 0.000 HIS J 45 PHE 0.020 0.001 PHE A 160 TYR 0.031 0.001 TYR K 129 ARG 0.005 0.000 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 1553) hydrogen bonds : angle 3.69601 ( 4584) SS BOND : bond 0.00375 ( 21) SS BOND : angle 1.07004 ( 42) covalent geometry : bond 0.00247 (25076) covalent geometry : angle 0.56912 (34115) *********************** 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 252 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 163 time to evaluate : 3.018 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: 0.8741 (OUTLIER) cc_final: 0.8250 (mp) REVERT: A 227 ASN cc_start: 0.8300 (m-40) cc_final: 0.7985 (t0) REVERT: B 74 MET cc_start: 0.7992 (tmm) cc_final: 0.7672 (tmm) REVERT: B 214 THR cc_start: 0.7253 (OUTLIER) cc_final: 0.7040 (p) REVERT: C 181 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7297 (ttp80) REVERT: C 187 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8259 (t80) REVERT: D 45 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.6264 (t-90) REVERT: E 203 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8256 (tptp) REVERT: G 258 LYS cc_start: 0.7405 (mmmt) cc_final: 0.7094 (mmmt) REVERT: H 204 CYS cc_start: 0.8902 (p) cc_final: 0.8556 (p) REVERT: H 259 ASP cc_start: 0.8114 (p0) cc_final: 0.7578 (p0) REVERT: I 262 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7772 (pm20) REVERT: J 256 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8360 (pp) REVERT: K 181 HIS cc_start: 0.7960 (m90) cc_final: 0.7337 (m-70) REVERT: K 246 HIS cc_start: 0.7601 (t-90) cc_final: 0.7051 (t70) REVERT: K 249 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7739 (mmmt) REVERT: M 83 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6879 (mmp) outliers start: 89 outliers final: 71 residues processed: 242 average time/residue: 0.3214 time to fit residues: 128.6676 Evaluate side-chains 232 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 151 time to evaluate : 2.629 ------------------------------------------------------------------------------- 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 172 LEU 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 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 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 66 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 212 LEU 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 212 LEU 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 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 119 VAL 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 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 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 151 SER 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 6 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 106 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.127283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.100057 restraints weight = 74592.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.097142 restraints weight = 69445.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.098427 restraints weight = 57859.751| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25097 Z= 0.154 Angle : 0.597 11.873 34157 Z= 0.299 Chirality : 0.039 0.241 3818 Planarity : 0.003 0.038 4341 Dihedral : 3.764 23.575 3390 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.55 % Allowed : 20.89 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.16), residues: 3034 helix: 2.18 (0.11), residues: 2048 sheet: 1.10 (0.53), residues: 78 loop : -0.96 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP K 118 HIS 0.003 0.001 HIS J 238 PHE 0.022 0.001 PHE C 200 TYR 0.032 0.002 TYR K 129 ARG 0.004 0.000 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 1553) hydrogen bonds : angle 3.77171 ( 4584) SS BOND : bond 0.00387 ( 21) SS BOND : angle 1.07209 ( 42) covalent geometry : bond 0.00342 (25076) covalent geometry : angle 0.59668 (34115) *********************** 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 243 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 151 time to evaluate : 2.968 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: 0.8822 (OUTLIER) cc_final: 0.8341 (mp) REVERT: A 227 ASN cc_start: 0.8269 (m-40) cc_final: 0.8027 (t0) REVERT: B 214 THR cc_start: 0.7254 (OUTLIER) cc_final: 0.7028 (p) REVERT: C 181 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7334 (ttp80) REVERT: C 187 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8351 (t80) REVERT: D 45 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.6382 (t-90) REVERT: E 203 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8243 (tptp) REVERT: G 291 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8001 (tm-30) REVERT: H 204 CYS cc_start: 0.8913 (p) cc_final: 0.8602 (p) REVERT: H 259 ASP cc_start: 0.8240 (p0) cc_final: 0.7696 (p0) REVERT: I 262 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: J 187 PHE cc_start: 0.7718 (m-80) cc_final: 0.6890 (m-80) REVERT: J 256 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8383 (pp) REVERT: K 181 HIS cc_start: 0.8051 (m90) cc_final: 0.7435 (m-70) REVERT: K 246 HIS cc_start: 0.7676 (t-90) cc_final: 0.7222 (t70) REVERT: M 83 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6955 (mmp) outliers start: 92 outliers final: 73 residues processed: 233 average time/residue: 0.3218 time to fit residues: 124.2450 Evaluate side-chains 227 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 145 time to evaluate : 2.843 ------------------------------------------------------------------------------- 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 141 HIS Chi-restraints excluded: chain A residue 172 LEU 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 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 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 66 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 212 LEU 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 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 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 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 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 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 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 256 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 127 THR Chi-restraints excluded: chain K residue 170 VAL 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 266 optimal weight: 7.9990 chunk 139 optimal weight: 0.4980 chunk 208 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 219 optimal weight: 0.2980 chunk 169 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.128842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.095013 restraints weight = 74059.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.094679 restraints weight = 41955.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.094910 restraints weight = 29598.737| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25097 Z= 0.107 Angle : 0.578 11.849 34157 Z= 0.283 Chirality : 0.037 0.190 3818 Planarity : 0.003 0.039 4341 Dihedral : 3.663 24.371 3390 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.66 % Allowed : 21.94 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.16), residues: 3034 helix: 2.30 (0.11), residues: 2049 sheet: 1.22 (0.54), residues: 78 loop : -0.91 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP K 118 HIS 0.008 0.001 HIS J 207 PHE 0.021 0.001 PHE C 200 TYR 0.032 0.001 TYR K 129 ARG 0.013 0.000 ARG M 38 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 1553) hydrogen bonds : angle 3.60108 ( 4584) SS BOND : bond 0.00328 ( 21) SS BOND : angle 1.18070 ( 42) covalent geometry : bond 0.00225 (25076) covalent geometry : angle 0.57719 (34115) ********************** 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 237 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 168 time to evaluate : 2.932 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: A 22 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8308 (mp) REVERT: A 187 MET cc_start: 0.7547 (mmm) cc_final: 0.7160 (mtp) REVERT: A 227 ASN cc_start: 0.8338 (m-40) cc_final: 0.8084 (t0) REVERT: C 181 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7448 (ttp80) REVERT: C 187 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8324 (t80) REVERT: D 45 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.6400 (t-90) REVERT: H 204 CYS cc_start: 0.8964 (p) cc_final: 0.8608 (p) REVERT: H 259 ASP cc_start: 0.7880 (p0) cc_final: 0.7312 (p0) REVERT: I 58 LEU cc_start: 0.8717 (tt) cc_final: 0.8388 (mm) REVERT: I 262 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: J 256 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8355 (pp) REVERT: K 181 HIS cc_start: 0.8221 (m90) cc_final: 0.7683 (m-70) REVERT: K 246 HIS cc_start: 0.7958 (t-90) cc_final: 0.7399 (t-170) REVERT: M 83 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7123 (mmp) REVERT: M 94 TYR cc_start: 0.8355 (m-10) cc_final: 0.7829 (m-80) outliers start: 69 outliers final: 55 residues processed: 229 average time/residue: 0.3121 time to fit residues: 119.7995 Evaluate side-chains 216 residues out of total 2627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 154 time to evaluate : 3.097 ------------------------------------------------------------------------------- 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 141 HIS Chi-restraints excluded: chain A residue 172 LEU 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 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 180 LEU Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 212 LEU 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 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 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 239 SER 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 119 VAL 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 256 LEU Chi-restraints excluded: chain K residue 26 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 259 optimal weight: 6.9990 chunk 287 optimal weight: 0.4980 chunk 173 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 176 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.129317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.101897 restraints weight = 74882.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.099608 restraints weight = 53536.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.100445 restraints weight = 48650.191| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25097 Z= 0.108 Angle : 0.580 11.552 34157 Z= 0.285 Chirality : 0.038 0.205 3818 Planarity : 0.003 0.039 4341 Dihedral : 3.626 23.514 3390 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.51 % Allowed : 22.21 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.16), residues: 3034 helix: 2.36 (0.12), residues: 2050 sheet: 1.09 (0.51), residues: 92 loop : -0.92 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP K 118 HIS 0.006 0.000 HIS J 207 PHE 0.020 0.001 PHE C 200 TYR 0.034 0.001 TYR K 129 ARG 0.012 0.000 ARG M 38 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 1553) hydrogen bonds : angle 3.55790 ( 4584) SS BOND : bond 0.00274 ( 21) SS BOND : angle 1.16215 ( 42) covalent geometry : bond 0.00233 (25076) covalent geometry : angle 0.57933 (34115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6600.38 seconds wall clock time: 117 minutes 18.99 seconds (7038.99 seconds total)