Starting phenix.real_space_refine on Mon Sep 14 07:00:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pif_20349/09_2026/6pif_20349.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pif_20349/09_2026/6pif_20349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pif_20349/09_2026/6pif_20349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pif_20349/09_2026/6pif_20349.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pif_20349/09_2026/6pif_20349.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pif_20349/09_2026/6pif_20349.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pif_20349/09_2026/6pif_20349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pif_20349/09_2026/6pif_20349.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 142 5.16 5 C 18194 2.51 5 N 5003 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28954 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2742 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2714 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2509 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 2 Chain: "G" Number of atoms: 4093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4093 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 21, 'TRANS': 495} Chain breaks: 1 Chain: "H" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1619 Classifications: {'peptide': 198} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Chain: "I" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2909 Classifications: {'peptide': 355} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 332} Chain breaks: 3 Chain: "J" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2982 Classifications: {'peptide': 368} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 347} Chain breaks: 2 Chain: "1" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNAv2': 60} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 14, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 23, 'rna3p': 36} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.86, per 1000 atoms: 0.20 Number of scatterers: 28954 At special positions: 0 Unit cell: (133, 164.35, 184.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 142 16.00 P 59 15.00 O 5556 8.00 N 5003 7.00 C 18194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 966.0 milliseconds 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6572 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 38 sheets defined 26.0% alpha, 13.0% beta 6 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.535A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.591A pdb=" N LEU A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.903A pdb=" N PHE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.661A pdb=" N ILE A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 321 removed outlier: 3.946A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 125 through 135 removed outlier: 4.007A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 264 through 269 removed outlier: 3.873A pdb=" N ILE B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 269' Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 330 through 343 removed outlier: 3.675A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.973A pdb=" N ALA C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.712A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.569A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.634A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.776A pdb=" N ILE C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.932A pdb=" N SER C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.898A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 269' Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.686A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.803A pdb=" N THR D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.842A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 264 through 269 removed outlier: 3.897A pdb=" N ILE D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.708A pdb=" N GLN D 311 " --> pdb=" O PHE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 319 removed outlier: 3.670A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 344 removed outlier: 3.504A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.846A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 123 Processing helix chain 'E' and resid 125 through 135 removed outlier: 3.519A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.648A pdb=" N LEU E 142 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.003A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 182' Processing helix chain 'E' and resid 183 through 187 removed outlier: 3.906A pdb=" N ASN E 186 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP E 187 " --> pdb=" O ASN E 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 183 through 187' Processing helix chain 'E' and resid 194 through 199 Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.600A pdb=" N ILE E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 319 " --> pdb=" O HIS E 315 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 320 " --> pdb=" O TYR E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 342 removed outlier: 3.700A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 Processing helix chain 'F' and resid 125 through 135 removed outlier: 4.068A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.913A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 264 through 269 removed outlier: 4.021A pdb=" N ILE F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 312 through 320 removed outlier: 3.682A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 320 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 344 removed outlier: 3.852A pdb=" N LYS F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 18 through 24 removed outlier: 4.050A pdb=" N PHE G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.516A pdb=" N VAL G 44 " --> pdb=" O LEU G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 76 Processing helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing helix chain 'G' and resid 130 through 134 Processing helix chain 'G' and resid 160 through 167 removed outlier: 3.501A pdb=" N LEU G 167 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 Processing helix chain 'G' and resid 219 through 228 removed outlier: 3.733A pdb=" N SER G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS G 224 " --> pdb=" O SER G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.538A pdb=" N MET G 252 " --> pdb=" O GLY G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 427 removed outlier: 3.829A pdb=" N PHE G 415 " --> pdb=" O SER G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 499 removed outlier: 3.684A pdb=" N VAL G 497 " --> pdb=" O GLN G 493 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 530 removed outlier: 3.713A pdb=" N GLU G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 558 removed outlier: 3.649A pdb=" N LEU G 553 " --> pdb=" O ASN G 549 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 31 removed outlier: 3.822A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 71 Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.693A pdb=" N LEU H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 30 through 45 removed outlier: 4.242A pdb=" N LEU I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU I 35 " --> pdb=" O HIS I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 82 removed outlier: 3.695A pdb=" N THR I 72 " --> pdb=" O SER I 68 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 206 Processing helix chain 'I' and resid 218 through 228 removed outlier: 3.693A pdb=" N GLY I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET I 228 " --> pdb=" O VAL I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 245 Processing helix chain 'I' and resid 246 through 248 No H-bonds generated for 'chain 'I' and resid 246 through 248' Processing helix chain 'I' and resid 249 through 265 removed outlier: 3.969A pdb=" N SER I 253 " --> pdb=" O ARG I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 removed outlier: 4.250A pdb=" N GLY I 301 " --> pdb=" O ASN I 297 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU I 302 " --> pdb=" O ILE I 298 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU I 303 " --> pdb=" O ILE I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 332 Processing helix chain 'I' and resid 337 through 345 Processing helix chain 'I' and resid 369 through 379 Processing helix chain 'J' and resid 14 through 23 removed outlier: 3.628A pdb=" N PHE J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 43 Processing helix chain 'J' and resid 67 through 81 removed outlier: 3.723A pdb=" N ALA J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 207 removed outlier: 3.622A pdb=" N GLY J 206 " --> pdb=" O ASN J 202 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS J 207 " --> pdb=" O TRP J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.607A pdb=" N ARG J 220 " --> pdb=" O PRO J 216 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 242 Processing helix chain 'J' and resid 246 through 261 removed outlier: 3.513A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE J 261 " --> pdb=" O ASP J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 310 removed outlier: 3.657A pdb=" N LEU J 303 " --> pdb=" O ILE J 299 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG J 310 " --> pdb=" O TYR J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 333 removed outlier: 3.739A pdb=" N MET J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 337 through 345 Processing helix chain 'J' and resid 369 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.597A pdb=" N SER A 88 " --> pdb=" O CYS A 19 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 151 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 166 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 41 removed outlier: 3.500A pdb=" N VAL A 73 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 removed outlier: 4.081A pdb=" N GLU A 254 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 15 Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 15 removed outlier: 3.733A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 42 Processing sheet with id=AA7, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.830A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 40 Processing sheet with id=AB2, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AB3, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.795A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AB6, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB7, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AB8, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AB9, first strand: chain 'E' and resid 13 through 14 removed outlier: 3.781A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AC2, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AC3, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AC4, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.891A pdb=" N CYS F 151 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 72 through 75 removed outlier: 7.394A pdb=" N ILE H 146 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR F 38 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AC9, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AD1, first strand: chain 'G' and resid 201 through 204 removed outlier: 3.726A pdb=" N GLY G 569 " --> pdb=" O ILE G 594 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 438 through 444 removed outlier: 6.560A pdb=" N VAL G 478 " --> pdb=" O HIS G 443 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU G 481 " --> pdb=" O PRO G 391 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU G 483 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL G 389 " --> pdb=" O LEU G 483 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 398 through 399 Processing sheet with id=AD4, first strand: chain 'G' and resid 457 through 458 Processing sheet with id=AD5, first strand: chain 'G' and resid 539 through 542 Processing sheet with id=AD6, first strand: chain 'G' and resid 615 through 616 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.664A pdb=" N VAL H 90 " --> pdb=" O TYR H 5 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 7 through 9 Processing sheet with id=AD9, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.599A pdb=" N ARG H 102 " --> pdb=" O ARG H 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.585A pdb=" N PHE I 367 " --> pdb=" O MET I 323 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 322 through 324 748 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5575 1.34 - 1.46: 7880 1.46 - 1.58: 16036 1.58 - 1.70: 118 1.70 - 1.82: 205 Bond restraints: 29814 Sorted by residual: bond pdb=" CD GLU D 127 " pdb=" OE1 GLU D 127 " ideal model delta sigma weight residual 1.249 1.415 -0.166 1.90e-02 2.77e+03 7.61e+01 bond pdb=" CD GLU D 127 " pdb=" OE2 GLU D 127 " ideal model delta sigma weight residual 1.249 1.378 -0.129 1.90e-02 2.77e+03 4.62e+01 bond pdb=" N GLY D 285 " pdb=" CA GLY D 285 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.98e+01 bond pdb=" N ILE B 258 " pdb=" CA ILE B 258 " ideal model delta sigma weight residual 1.460 1.497 -0.037 8.60e-03 1.35e+04 1.81e+01 bond pdb=" N ILE J 347 " pdb=" CA ILE J 347 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.80e+01 ... (remaining 29809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 28931 1.84 - 3.69: 10026 3.69 - 5.53: 1659 5.53 - 7.37: 117 7.37 - 9.22: 9 Bond angle restraints: 40742 Sorted by residual: angle pdb=" N PRO I 86 " pdb=" CA PRO I 86 " pdb=" CB PRO I 86 " ideal model delta sigma weight residual 103.08 97.36 5.72 9.70e-01 1.06e+00 3.48e+01 angle pdb=" N PRO G 533 " pdb=" CA PRO G 533 " pdb=" CB PRO G 533 " ideal model delta sigma weight residual 103.25 97.27 5.98 1.05e+00 9.07e-01 3.24e+01 angle pdb=" C CYS I 131 " pdb=" CA CYS I 131 " pdb=" CB CYS I 131 " ideal model delta sigma weight residual 117.23 109.68 7.55 1.36e+00 5.41e-01 3.08e+01 angle pdb=" CA GLY H 177 " pdb=" C GLY H 177 " pdb=" O GLY H 177 " ideal model delta sigma weight residual 122.33 117.88 4.45 8.10e-01 1.52e+00 3.02e+01 angle pdb=" N PRO D 276 " pdb=" CA PRO D 276 " pdb=" CB PRO D 276 " ideal model delta sigma weight residual 103.25 97.79 5.46 1.05e+00 9.07e-01 2.70e+01 ... (remaining 40737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.98: 16491 26.98 - 53.97: 941 53.97 - 80.95: 159 80.95 - 107.93: 13 107.93 - 134.91: 2 Dihedral angle restraints: 17606 sinusoidal: 7492 harmonic: 10114 Sorted by residual: dihedral pdb=" C4' G 1 53 " pdb=" C3' G 1 53 " pdb=" C2' G 1 53 " pdb=" C1' G 1 53 " ideal model delta sinusoidal sigma weight residual 36.34 -40.68 77.03 1 3.10e+00 1.04e-01 7.75e+02 dihedral pdb=" C4' G 1 15 " pdb=" C3' G 1 15 " pdb=" C2' G 1 15 " pdb=" C1' G 1 15 " ideal model delta sinusoidal sigma weight residual 36.34 -38.84 75.19 1 3.10e+00 1.04e-01 7.44e+02 dihedral pdb=" C4' U 1 9 " pdb=" C3' U 1 9 " pdb=" C2' U 1 9 " pdb=" C1' U 1 9 " ideal model delta sinusoidal sigma weight residual 36.35 -38.54 74.89 1 3.10e+00 1.04e-01 7.39e+02 ... (remaining 17603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2075 0.061 - 0.122: 1634 0.122 - 0.183: 593 0.183 - 0.244: 177 0.244 - 0.305: 24 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C2' C 1 28 " pdb=" C3' C 1 28 " pdb=" O2' C 1 28 " pdb=" C1' C 1 28 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA GLU I 85 " pdb=" N GLU I 85 " pdb=" C GLU I 85 " pdb=" CB GLU I 85 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA TYR I 140 " pdb=" N TYR I 140 " pdb=" C TYR I 140 " pdb=" CB TYR I 140 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 4500 not shown) Planarity restraints: 5002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 127 " -0.064 2.00e-02 2.50e+03 1.20e-01 1.44e+02 pdb=" CD GLU D 127 " 0.208 2.00e-02 2.50e+03 pdb=" OE1 GLU D 127 " -0.069 2.00e-02 2.50e+03 pdb=" OE2 GLU D 127 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 403 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C SER G 403 " -0.043 2.00e-02 2.50e+03 pdb=" O SER G 403 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO G 404 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 7 " 0.012 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C LYS I 7 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS I 7 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO I 8 " 0.013 2.00e-02 2.50e+03 ... (remaining 4999 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 30 1.99 - 2.71: 1050 2.71 - 3.44: 37507 3.44 - 4.17: 66348 4.17 - 4.90: 117979 Nonbonded interactions: 222914 Sorted by model distance: nonbonded pdb=" CG TYR H 5 " pdb=" CD1 ILE H 199 " model vdw 1.256 3.680 nonbonded pdb=" CE MET F 346 " pdb=" N1 U 1 35 " model vdw 1.271 3.540 nonbonded pdb=" CD1 ILE G 42 " pdb=" CB LEU G 56 " model vdw 1.282 3.860 nonbonded pdb=" O ASP G 48 " pdb=" ND2 ASN G 131 " model vdw 1.347 3.120 nonbonded pdb=" CE MET F 220 " pdb=" N7 G 1 41 " model vdw 1.376 3.540 ... (remaining 222909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'B' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'C' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'D' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'E' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 1 through 232 or resid 236 through 351 or resid 361 throug \ h 393)) selection = (chain 'J' and (resid 1 through 162 or resid 195 through 351 or resid 361 throug \ h 393)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.860 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.014 0.406 29816 Z= 1.063 Angle : 1.753 9.218 40742 Z= 1.226 Chirality : 0.091 0.305 4503 Planarity : 0.004 0.120 5002 Dihedral : 16.802 134.913 11034 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 3.91 % Allowed : 14.76 % Favored : 81.32 % Rotamer: Outliers : 2.17 % Allowed : 6.20 % Favored : 91.63 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.80 % Twisted Proline : 6.06 % Twisted General : 2.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.83 (0.11), residues: 3400 helix: -2.66 (0.14), residues: 880 sheet: -1.93 (0.21), residues: 477 loop : -4.02 (0.11), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 178 TYR 0.025 0.002 TYR I 101 PHE 0.019 0.002 PHE I 144 TRP 0.031 0.002 TRP A 24 HIS 0.009 0.002 HIS E 299 Details of bonding type rmsd/Z covalent geometry : bond 0.01367 / 1.04 (29814) covalent geometry : angle 1.75275 / 1.23 (40742) hydrogen bonds : bond 0.21182 / 14.09 ( 753) hydrogen bonds : angle 8.79432 / 6.00 ( 2089) Misc. bond : bond 0.28916 / 15.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 643 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 42 GLN cc_start: 0.7782 (pt0) cc_final: 0.7581 (pt0) REVERT: A 293 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5839 (p0) REVERT: B 43 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7894 (mmt) REVERT: B 134 MET cc_start: 0.8398 (mtm) cc_final: 0.8003 (mtp) REVERT: B 333 ASP cc_start: 0.8388 (m-30) cc_final: 0.8150 (m-30) REVERT: C 210 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7435 (ptp90) REVERT: C 244 ARG cc_start: 0.8540 (mtp-110) cc_final: 0.8194 (ttm170) REVERT: C 324 LYS cc_start: 0.7295 (tppt) cc_final: 0.6639 (tptm) REVERT: D 71 HIS cc_start: 0.6693 (m-70) cc_final: 0.6329 (t-170) REVERT: D 120 GLU cc_start: 0.8012 (tt0) cc_final: 0.7643 (tm-30) REVERT: D 291 ARG cc_start: 0.7659 (ttt90) cc_final: 0.7127 (ttp-170) REVERT: F 6 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7074 (m-40) REVERT: F 71 HIS cc_start: 0.6126 (t-90) cc_final: 0.5684 (t-90) REVERT: F 88 SER cc_start: 0.7864 (t) cc_final: 0.7389 (p) REVERT: F 195 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7686 (ttmm) REVERT: F 210 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7324 (ttm-80) REVERT: F 263 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8105 (tptt) REVERT: F 308 SER cc_start: 0.8416 (m) cc_final: 0.7847 (t) REVERT: G 47 THR cc_start: 0.7177 (OUTLIER) cc_final: 0.6871 (t) REVERT: G 190 ASN cc_start: 0.7309 (t0) cc_final: 0.6925 (m110) REVERT: G 205 ASP cc_start: 0.7884 (p0) cc_final: 0.7615 (p0) REVERT: G 469 THR cc_start: 0.7726 (p) cc_final: 0.7351 (p) REVERT: G 613 PHE cc_start: 0.7354 (m-80) cc_final: 0.6850 (m-80) REVERT: H 77 GLN cc_start: 0.7609 (tp-100) cc_final: 0.7318 (mt0) REVERT: H 81 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8369 (pp) REVERT: H 127 LEU cc_start: 0.6116 (mm) cc_final: 0.5639 (pp) REVERT: I 1 MET cc_start: 0.0525 (tpt) cc_final: 0.0163 (mmm) REVERT: I 57 THR cc_start: 0.5045 (m) cc_final: 0.4769 (p) REVERT: I 130 LEU cc_start: 0.2321 (OUTLIER) cc_final: 0.1985 (mm) REVERT: I 198 CYS cc_start: 0.5893 (OUTLIER) cc_final: 0.5413 (t) REVERT: I 272 GLU cc_start: 0.7840 (pt0) cc_final: 0.7570 (mp0) REVERT: I 383 ASP cc_start: 0.7937 (p0) cc_final: 0.7729 (p0) REVERT: I 386 ASN cc_start: 0.8150 (t0) cc_final: 0.7949 (t0) REVERT: J 43 ASP cc_start: 0.7734 (m-30) cc_final: 0.7326 (m-30) REVERT: J 47 ASN cc_start: 0.7750 (p0) cc_final: 0.7530 (m-40) REVERT: J 217 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7294 (tttt) outliers start: 66 outliers final: 25 residues processed: 694 average time/residue: 0.2004 time to fit residues: 213.7342 Evaluate side-chains 357 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 276 PRO Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 276 PRO Chi-restraints excluded: chain E residue 276 PRO Chi-restraints excluded: chain F residue 6 ASN Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 276 PRO Chi-restraints excluded: chain F residue 346 MET Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain G residue 533 PRO Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 117 ARG Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 108 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 174 ASN A 218 ASN B 183 ASN B 311 GLN B 312 GLN C 104 ASN C 174 ASN C 311 GLN C 323 ASN D 174 ASN D 183 ASN E 214 HIS E 241 GLN E 311 GLN F 183 ASN F 218 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 315 HIS G 180 GLN G 196 ASN G 227 GLN G 392 ASN G 444 GLN H 88 ASN H 132 GLN I 80 GLN I 84 ASN I 265 HIS I 386 ASN J 46 HIS J 95 ASN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.121204 restraints weight = 44379.444| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.66 r_work: 0.3134 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29816 Z= 0.186 Angle : 1.026 23.110 40742 Z= 0.487 Chirality : 0.069 0.922 4503 Planarity : 0.005 0.092 5002 Dihedral : 14.055 157.784 4504 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 1.03 % Allowed : 13.68 % Favored : 85.29 % Rotamer: Outliers : 2.92 % Allowed : 11.48 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 5.45 % Twisted General : 1.72 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.13), residues: 3400 helix: -1.50 (0.16), residues: 912 sheet: -1.01 (0.23), residues: 471 loop : -3.77 (0.11), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 244 TYR 0.023 0.002 TYR J 169 PHE 0.019 0.002 PHE I 244 TRP 0.041 0.002 TRP A 24 HIS 0.010 0.001 HIS G 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (29814) covalent geometry : angle 1.02614 / 0.49 (40742) hydrogen bonds : bond 0.04282 / 2.87 ( 753) hydrogen bonds : angle 5.73159 / 3.97 ( 2089) Misc. bond : bond 0.00604 / 0.31 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 361 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 VAL cc_start: 0.6702 (OUTLIER) cc_final: 0.6448 (m) REVERT: A 114 GLN cc_start: 0.8030 (tp40) cc_final: 0.7712 (tp-100) REVERT: A 202 ASP cc_start: 0.6841 (m-30) cc_final: 0.6630 (t0) REVERT: B 17 ASP cc_start: 0.8449 (p0) cc_final: 0.8129 (p0) REVERT: B 185 LYS cc_start: 0.5404 (pttm) cc_final: 0.5062 (mtmt) REVERT: C 252 ASP cc_start: 0.8132 (m-30) cc_final: 0.7915 (t0) REVERT: D 71 HIS cc_start: 0.7665 (m-70) cc_final: 0.7240 (t-170) REVERT: F 188 SER cc_start: 0.8684 (m) cc_final: 0.8475 (p) REVERT: F 210 ARG cc_start: 0.8237 (ttm-80) cc_final: 0.8022 (ttm170) REVERT: F 263 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8188 (tptt) REVERT: G 19 LEU cc_start: 0.8351 (tp) cc_final: 0.7807 (tp) REVERT: G 23 PHE cc_start: 0.8163 (m-80) cc_final: 0.7814 (m-80) REVERT: G 36 GLU cc_start: 0.4709 (OUTLIER) cc_final: 0.4370 (mp0) REVERT: G 190 ASN cc_start: 0.7550 (t0) cc_final: 0.7101 (m-40) REVERT: H 29 HIS cc_start: 0.7794 (t70) cc_final: 0.7541 (t70) REVERT: H 127 LEU cc_start: 0.6013 (mm) cc_final: 0.5635 (pp) REVERT: H 160 ASN cc_start: 0.7448 (m-40) cc_final: 0.7160 (m110) REVERT: H 197 PRO cc_start: 0.8758 (Cg_endo) cc_final: 0.8208 (Cg_exo) REVERT: I 3 LEU cc_start: 0.4865 (tp) cc_final: 0.3770 (mt) REVERT: I 84 ASN cc_start: 0.4898 (OUTLIER) cc_final: 0.4538 (t0) REVERT: I 198 CYS cc_start: 0.6355 (OUTLIER) cc_final: 0.5760 (t) REVERT: I 217 LYS cc_start: 0.7184 (mtpt) cc_final: 0.6904 (mttp) REVERT: I 272 GLU cc_start: 0.8089 (pt0) cc_final: 0.7747 (mp0) REVERT: I 386 ASN cc_start: 0.8236 (t0) cc_final: 0.8010 (t0) REVERT: J 41 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8670 (mt) REVERT: J 43 ASP cc_start: 0.8057 (m-30) cc_final: 0.7612 (m-30) REVERT: J 47 ASN cc_start: 0.8168 (p0) cc_final: 0.7865 (m-40) REVERT: J 85 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7945 (mp0) REVERT: J 108 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7437 (m) REVERT: J 323 MET cc_start: 0.4931 (tpp) cc_final: 0.4708 (tpp) REVERT: J 367 PHE cc_start: 0.7028 (m-10) cc_final: 0.6802 (m-10) outliers start: 89 outliers final: 44 residues processed: 429 average time/residue: 0.1767 time to fit residues: 121.9460 Evaluate side-chains 330 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 218 ASN Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 392 ASN Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 517 LYS Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 348 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 181 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 285 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 110 GLN A 311 GLN ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 299 HIS ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 349 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 315 HIS G 131 ASN G 384 ASN G 548 ASN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 73 HIS I 31 HIS I 151 HIS I 296 HIS ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 HIS ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.147644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112098 restraints weight = 44695.123| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.78 r_work: 0.3029 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 29816 Z= 0.269 Angle : 0.956 14.020 40742 Z= 0.470 Chirality : 0.064 0.625 4503 Planarity : 0.006 0.066 5002 Dihedral : 14.110 162.326 4459 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.91 % Allowed : 15.91 % Favored : 83.18 % Rotamer: Outliers : 3.77 % Allowed : 14.07 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 4.85 % Twisted General : 1.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.13), residues: 3400 helix: -1.27 (0.17), residues: 924 sheet: -0.76 (0.23), residues: 464 loop : -3.70 (0.11), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 628 TYR 0.021 0.002 TYR H 74 PHE 0.026 0.002 PHE G 613 TRP 0.025 0.002 TRP I 203 HIS 0.019 0.002 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.27 (29814) covalent geometry : angle 0.95552 / 0.47 (40742) hydrogen bonds : bond 0.04525 / 3.01 ( 753) hydrogen bonds : angle 5.45603 / 3.76 ( 2089) Misc. bond : bond 0.00168 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 307 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 VAL cc_start: 0.6655 (OUTLIER) cc_final: 0.6422 (m) REVERT: A 114 GLN cc_start: 0.8091 (tp40) cc_final: 0.7774 (tp-100) REVERT: A 202 ASP cc_start: 0.6852 (m-30) cc_final: 0.6579 (t0) REVERT: A 307 PHE cc_start: 0.8368 (m-10) cc_final: 0.8101 (m-10) REVERT: C 252 ASP cc_start: 0.8124 (m-30) cc_final: 0.7840 (t0) REVERT: D 71 HIS cc_start: 0.7909 (m-70) cc_final: 0.7653 (m170) REVERT: E 252 ASP cc_start: 0.8692 (t0) cc_final: 0.8306 (t0) REVERT: F 263 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8411 (tptt) REVERT: G 19 LEU cc_start: 0.8362 (tp) cc_final: 0.7590 (tp) REVERT: G 23 PHE cc_start: 0.8070 (m-80) cc_final: 0.7384 (m-80) REVERT: G 231 ASP cc_start: 0.7628 (m-30) cc_final: 0.7269 (p0) REVERT: G 252 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8404 (ptm) REVERT: H 16 ASN cc_start: 0.8430 (t0) cc_final: 0.8091 (t0) REVERT: H 29 HIS cc_start: 0.8174 (t70) cc_final: 0.7962 (t-90) REVERT: H 81 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8617 (pp) REVERT: H 88 ASN cc_start: 0.7332 (m-40) cc_final: 0.6745 (t0) REVERT: H 127 LEU cc_start: 0.6063 (mm) cc_final: 0.5745 (pp) REVERT: H 164 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6885 (mtp180) REVERT: H 181 PHE cc_start: 0.4741 (OUTLIER) cc_final: 0.3692 (p90) REVERT: H 194 GLN cc_start: 0.7459 (pp30) cc_final: 0.7185 (pp30) REVERT: I 3 LEU cc_start: 0.5155 (tp) cc_final: 0.3751 (mt) REVERT: I 198 CYS cc_start: 0.6503 (OUTLIER) cc_final: 0.6095 (t) REVERT: I 217 LYS cc_start: 0.7446 (mtpt) cc_final: 0.7141 (mttp) REVERT: I 239 SER cc_start: 0.5101 (m) cc_final: 0.4770 (t) REVERT: I 272 GLU cc_start: 0.8205 (pt0) cc_final: 0.7818 (mp0) REVERT: J 43 ASP cc_start: 0.8018 (m-30) cc_final: 0.7725 (m-30) REVERT: J 47 ASN cc_start: 0.8263 (p0) cc_final: 0.7872 (m-40) REVERT: J 153 HIS cc_start: 0.6093 (OUTLIER) cc_final: 0.5810 (p-80) REVERT: J 158 ILE cc_start: 0.7085 (pt) cc_final: 0.6777 (mp) REVERT: J 163 CYS cc_start: 0.6285 (m) cc_final: 0.5993 (m) REVERT: J 308 GLU cc_start: 0.6193 (tm-30) cc_final: 0.5915 (tm-30) REVERT: J 323 MET cc_start: 0.5169 (tpp) cc_final: 0.4955 (tpp) outliers start: 115 outliers final: 61 residues processed: 402 average time/residue: 0.1704 time to fit residues: 111.5093 Evaluate side-chains 327 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 258 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 448 GLU Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 137 TYR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 241 VAL Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 348 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 274 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 10 optimal weight: 0.0030 chunk 83 optimal weight: 4.9990 chunk 243 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 317 optimal weight: 20.0000 overall best weight: 2.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS G 196 ASN G 392 ASN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS H 132 GLN I 84 ASN I 154 ASN ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.149749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114140 restraints weight = 44270.777| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.77 r_work: 0.3062 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29816 Z= 0.181 Angle : 0.854 13.981 40742 Z= 0.423 Chirality : 0.057 0.530 4503 Planarity : 0.005 0.061 5002 Dihedral : 13.745 163.960 4458 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.88 % Allowed : 14.47 % Favored : 84.65 % Rotamer: Outliers : 3.74 % Allowed : 14.76 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 4.24 % Twisted General : 1.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.13), residues: 3400 helix: -1.10 (0.17), residues: 924 sheet: -0.94 (0.23), residues: 494 loop : -3.54 (0.12), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 286 TYR 0.023 0.001 TYR G 197 PHE 0.034 0.002 PHE I 238 TRP 0.027 0.001 TRP I 203 HIS 0.013 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (29814) covalent geometry : angle 0.85364 / 0.42 (40742) hydrogen bonds : bond 0.03749 / 2.50 ( 753) hydrogen bonds : angle 5.26722 / 3.64 ( 2089) Misc. bond : bond 0.00360 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 288 time to evaluate : 1.069 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: A 114 GLN cc_start: 0.8189 (tp40) cc_final: 0.7919 (tp-100) REVERT: A 202 ASP cc_start: 0.6856 (m-30) cc_final: 0.6495 (t0) REVERT: A 307 PHE cc_start: 0.8222 (m-10) cc_final: 0.7917 (m-10) REVERT: B 17 ASP cc_start: 0.8598 (p0) cc_final: 0.8303 (p0) REVERT: B 138 ASN cc_start: 0.8590 (p0) cc_final: 0.8098 (p0) REVERT: C 252 ASP cc_start: 0.8072 (m-30) cc_final: 0.7827 (t0) REVERT: C 291 ARG cc_start: 0.7405 (ttt-90) cc_final: 0.7061 (ttp80) REVERT: D 71 HIS cc_start: 0.7745 (m-70) cc_final: 0.7396 (t70) REVERT: D 210 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8114 (ttm110) REVERT: E 252 ASP cc_start: 0.8648 (t0) cc_final: 0.8279 (t0) REVERT: E 333 ASP cc_start: 0.8204 (m-30) cc_final: 0.7959 (m-30) REVERT: F 37 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7181 (mtp180) REVERT: F 135 ASN cc_start: 0.8439 (p0) cc_final: 0.8138 (p0) REVERT: F 263 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8443 (tptt) REVERT: G 23 PHE cc_start: 0.8040 (m-80) cc_final: 0.7425 (m-80) REVERT: G 231 ASP cc_start: 0.7478 (m-30) cc_final: 0.7233 (p0) REVERT: H 16 ASN cc_start: 0.8474 (t0) cc_final: 0.8101 (t0) REVERT: H 81 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8623 (pp) REVERT: H 88 ASN cc_start: 0.7296 (m-40) cc_final: 0.6711 (t0) REVERT: H 105 GLN cc_start: 0.8724 (tt0) cc_final: 0.8418 (tt0) REVERT: H 181 PHE cc_start: 0.4622 (OUTLIER) cc_final: 0.4125 (p90) REVERT: H 190 GLU cc_start: 0.5708 (pt0) cc_final: 0.5403 (pt0) REVERT: I 1 MET cc_start: 0.1808 (tpp) cc_final: -0.0644 (tpt) REVERT: I 84 ASN cc_start: 0.4968 (OUTLIER) cc_final: 0.4638 (t0) REVERT: I 110 ARG cc_start: 0.5802 (tpm170) cc_final: 0.4275 (tpm170) REVERT: I 198 CYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6611 (t) REVERT: I 217 LYS cc_start: 0.7455 (mtpt) cc_final: 0.7150 (mttp) REVERT: I 239 SER cc_start: 0.4846 (m) cc_final: 0.4569 (t) REVERT: I 272 GLU cc_start: 0.8203 (pt0) cc_final: 0.7802 (mp0) REVERT: J 43 ASP cc_start: 0.7875 (m-30) cc_final: 0.7594 (m-30) REVERT: J 153 HIS cc_start: 0.5899 (OUTLIER) cc_final: 0.5587 (p-80) REVERT: J 308 GLU cc_start: 0.6016 (tm-30) cc_final: 0.5779 (tm-30) REVERT: J 323 MET cc_start: 0.5340 (tpp) cc_final: 0.5106 (tpp) outliers start: 114 outliers final: 67 residues processed: 379 average time/residue: 0.1653 time to fit residues: 102.9661 Evaluate side-chains 328 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 254 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 137 TYR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 58 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 chunk 270 optimal weight: 30.0000 chunk 22 optimal weight: 0.5980 chunk 218 optimal weight: 10.0000 chunk 342 optimal weight: 6.9990 chunk 138 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 overall best weight: 2.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 HIS ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.149826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115048 restraints weight = 44270.898| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.73 r_work: 0.3066 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29816 Z= 0.174 Angle : 0.831 14.004 40742 Z= 0.411 Chirality : 0.055 0.472 4503 Planarity : 0.005 0.059 5002 Dihedral : 13.489 164.669 4452 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.76 % Allowed : 15.03 % Favored : 84.21 % Rotamer: Outliers : 3.61 % Allowed : 15.55 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.64 % Twisted General : 1.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.13), residues: 3400 helix: -0.98 (0.17), residues: 927 sheet: -0.81 (0.22), residues: 504 loop : -3.49 (0.12), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 503 TYR 0.038 0.002 TYR G 197 PHE 0.030 0.001 PHE I 238 TRP 0.028 0.001 TRP I 203 HIS 0.007 0.001 HIS D 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (29814) covalent geometry : angle 0.83058 / 0.41 (40742) hydrogen bonds : bond 0.03617 / 2.42 ( 753) hydrogen bonds : angle 5.17103 / 3.57 ( 2089) Misc. bond : bond 0.00266 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 285 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8162 (tp40) cc_final: 0.7866 (tp-100) REVERT: A 202 ASP cc_start: 0.7020 (m-30) cc_final: 0.6488 (t0) REVERT: A 307 PHE cc_start: 0.8239 (m-10) cc_final: 0.7912 (m-10) REVERT: B 17 ASP cc_start: 0.8599 (p0) cc_final: 0.8293 (p0) REVERT: B 138 ASN cc_start: 0.8587 (p0) cc_final: 0.8006 (p0) REVERT: C 252 ASP cc_start: 0.8102 (m-30) cc_final: 0.7824 (t0) REVERT: C 291 ARG cc_start: 0.7439 (ttt-90) cc_final: 0.7127 (ttp80) REVERT: C 347 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8514 (m-80) REVERT: D 71 HIS cc_start: 0.7762 (m-70) cc_final: 0.7440 (t-170) REVERT: E 252 ASP cc_start: 0.8617 (t0) cc_final: 0.8255 (t0) REVERT: E 333 ASP cc_start: 0.8168 (m-30) cc_final: 0.7924 (m-30) REVERT: F 37 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7239 (mtp180) REVERT: F 135 ASN cc_start: 0.8442 (p0) cc_final: 0.8193 (p0) REVERT: F 263 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8450 (tptt) REVERT: F 291 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7797 (ttt180) REVERT: G 23 PHE cc_start: 0.8066 (m-80) cc_final: 0.7798 (m-80) REVERT: G 35 ASN cc_start: 0.4724 (OUTLIER) cc_final: 0.4429 (m110) REVERT: H 16 ASN cc_start: 0.8530 (t0) cc_final: 0.8183 (t0) REVERT: H 77 GLN cc_start: 0.7496 (tp-100) cc_final: 0.7083 (mt0) REVERT: H 78 MET cc_start: 0.7364 (tpp) cc_final: 0.7091 (tpp) REVERT: H 81 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8612 (pp) REVERT: H 88 ASN cc_start: 0.7258 (m-40) cc_final: 0.6658 (t0) REVERT: H 105 GLN cc_start: 0.8745 (tt0) cc_final: 0.8544 (tt0) REVERT: H 164 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6485 (mtp180) REVERT: H 176 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5595 (pt0) REVERT: I 1 MET cc_start: 0.1590 (tpp) cc_final: -0.0727 (tpt) REVERT: I 3 LEU cc_start: 0.4359 (OUTLIER) cc_final: 0.3861 (mt) REVERT: I 198 CYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6933 (t) REVERT: I 217 LYS cc_start: 0.7495 (mtpt) cc_final: 0.7193 (mttp) REVERT: I 272 GLU cc_start: 0.8149 (pt0) cc_final: 0.7803 (mp0) REVERT: J 43 ASP cc_start: 0.7972 (m-30) cc_final: 0.7686 (m-30) REVERT: J 308 GLU cc_start: 0.6094 (tm-30) cc_final: 0.5833 (tm-30) outliers start: 110 outliers final: 69 residues processed: 374 average time/residue: 0.1687 time to fit residues: 103.8296 Evaluate side-chains 336 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 257 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 291 ARG Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 198 CYS Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 331 MET Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 119 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 227 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 309 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 ASN G 226 HIS ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS I 84 ASN I 145 GLN ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 HIS J 386 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115204 restraints weight = 44082.378| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.66 r_work: 0.3101 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29816 Z= 0.167 Angle : 0.826 15.328 40742 Z= 0.407 Chirality : 0.054 0.434 4503 Planarity : 0.005 0.062 5002 Dihedral : 13.291 165.968 4450 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.65 % Allowed : 14.97 % Favored : 84.38 % Rotamer: Outliers : 3.87 % Allowed : 16.47 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 2.42 % Twisted General : 1.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.14), residues: 3400 helix: -0.84 (0.17), residues: 924 sheet: -0.67 (0.23), residues: 499 loop : -3.40 (0.12), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 503 TYR 0.035 0.001 TYR G 197 PHE 0.024 0.001 PHE I 238 TRP 0.025 0.001 TRP A 24 HIS 0.007 0.001 HIS H 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (29814) covalent geometry : angle 0.82646 / 0.41 (40742) hydrogen bonds : bond 0.03457 / 2.30 ( 753) hydrogen bonds : angle 5.12407 / 3.53 ( 2089) Misc. bond : bond 0.00816 / 0.39 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 287 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8099 (tp40) cc_final: 0.7819 (tp-100) REVERT: B 17 ASP cc_start: 0.8566 (p0) cc_final: 0.8241 (p0) REVERT: B 138 ASN cc_start: 0.8456 (p0) cc_final: 0.7936 (p0) REVERT: C 252 ASP cc_start: 0.8089 (m-30) cc_final: 0.7813 (t0) REVERT: C 291 ARG cc_start: 0.7419 (ttt-90) cc_final: 0.7140 (ttp80) REVERT: C 347 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: D 71 HIS cc_start: 0.7645 (m-70) cc_final: 0.7392 (t-170) REVERT: E 252 ASP cc_start: 0.8593 (t0) cc_final: 0.8237 (t0) REVERT: F 37 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7219 (mtp180) REVERT: F 43 MET cc_start: 0.5849 (mpp) cc_final: 0.5235 (mpp) REVERT: F 135 ASN cc_start: 0.8451 (p0) cc_final: 0.8148 (p0) REVERT: F 263 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8440 (tptt) REVERT: G 21 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6810 (ptm160) REVERT: G 23 PHE cc_start: 0.8083 (m-80) cc_final: 0.7795 (m-80) REVERT: G 592 GLU cc_start: 0.7296 (tt0) cc_final: 0.7068 (mt-10) REVERT: G 622 TYR cc_start: 0.7807 (p90) cc_final: 0.7590 (p90) REVERT: H 16 ASN cc_start: 0.8518 (t0) cc_final: 0.8192 (t0) REVERT: H 33 TYR cc_start: 0.6041 (OUTLIER) cc_final: 0.5831 (m-80) REVERT: H 77 GLN cc_start: 0.7521 (tp-100) cc_final: 0.7079 (mt0) REVERT: H 88 ASN cc_start: 0.7400 (m-40) cc_final: 0.6793 (t0) REVERT: H 105 GLN cc_start: 0.8733 (tt0) cc_final: 0.8453 (tt0) REVERT: H 164 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6379 (mtp180) REVERT: H 176 GLU cc_start: 0.5892 (OUTLIER) cc_final: 0.3831 (tm-30) REVERT: I 1 MET cc_start: 0.2019 (tpp) cc_final: -0.0125 (tpt) REVERT: I 3 LEU cc_start: 0.4477 (OUTLIER) cc_final: 0.4253 (mt) REVERT: I 217 LYS cc_start: 0.7513 (mtpt) cc_final: 0.7211 (mttp) REVERT: I 272 GLU cc_start: 0.8043 (pt0) cc_final: 0.7771 (mp0) REVERT: J 43 ASP cc_start: 0.7976 (m-30) cc_final: 0.7681 (m-30) REVERT: J 308 GLU cc_start: 0.6071 (tm-30) cc_final: 0.5777 (tm-30) REVERT: J 323 MET cc_start: 0.4475 (tpp) cc_final: 0.4139 (tpp) outliers start: 118 outliers final: 81 residues processed: 379 average time/residue: 0.1705 time to fit residues: 105.9528 Evaluate side-chains 345 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 256 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 238 PHE Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 289 optimal weight: 4.9990 chunk 303 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 294 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 110 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 518 HIS ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS I 143 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.149129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114411 restraints weight = 44366.286| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.68 r_work: 0.3072 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29816 Z= 0.195 Angle : 0.844 13.686 40742 Z= 0.415 Chirality : 0.056 0.467 4503 Planarity : 0.005 0.071 5002 Dihedral : 13.243 164.314 4447 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.62 % Allowed : 15.82 % Favored : 83.56 % Rotamer: Outliers : 3.67 % Allowed : 17.52 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 1.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.14), residues: 3400 helix: -0.80 (0.17), residues: 929 sheet: -0.63 (0.23), residues: 497 loop : -3.36 (0.12), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 291 TYR 0.037 0.002 TYR G 197 PHE 0.033 0.002 PHE I 238 TRP 0.022 0.001 TRP G 161 HIS 0.014 0.001 HIS G 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (29814) covalent geometry : angle 0.84371 / 0.42 (40742) hydrogen bonds : bond 0.03633 / 2.42 ( 753) hydrogen bonds : angle 5.11032 / 3.51 ( 2089) Misc. bond : bond 0.00692 / 0.33 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 271 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8150 (tp40) cc_final: 0.7894 (tp-100) REVERT: A 307 PHE cc_start: 0.8109 (m-10) cc_final: 0.7841 (m-10) REVERT: B 6 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8261 (t0) REVERT: B 138 ASN cc_start: 0.8501 (p0) cc_final: 0.7965 (p0) REVERT: C 252 ASP cc_start: 0.8095 (m-30) cc_final: 0.7829 (t0) REVERT: C 291 ARG cc_start: 0.7393 (ttt-90) cc_final: 0.7171 (ttp80) REVERT: C 347 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8533 (m-80) REVERT: D 71 HIS cc_start: 0.7720 (m-70) cc_final: 0.7450 (t-170) REVERT: E 252 ASP cc_start: 0.8625 (t0) cc_final: 0.8252 (t0) REVERT: F 43 MET cc_start: 0.5889 (mpp) cc_final: 0.5326 (mpp) REVERT: F 135 ASN cc_start: 0.8547 (p0) cc_final: 0.8221 (p0) REVERT: F 263 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8421 (tptt) REVERT: G 21 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6836 (ptm160) REVERT: G 622 TYR cc_start: 0.7897 (p90) cc_final: 0.7643 (p90) REVERT: H 3 TRP cc_start: 0.6271 (m-10) cc_final: 0.6042 (m-10) REVERT: H 77 GLN cc_start: 0.7397 (tp-100) cc_final: 0.7083 (mt0) REVERT: H 78 MET cc_start: 0.7337 (tpp) cc_final: 0.7098 (tpp) REVERT: H 88 ASN cc_start: 0.7433 (m-40) cc_final: 0.6803 (t0) REVERT: H 93 PRO cc_start: 0.5876 (Cg_exo) cc_final: 0.5643 (Cg_endo) REVERT: H 164 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6655 (mtp180) REVERT: H 194 GLN cc_start: 0.7597 (pp30) cc_final: 0.7104 (tm-30) REVERT: I 1 MET cc_start: 0.2110 (tpp) cc_final: -0.0030 (tpt) REVERT: I 3 LEU cc_start: 0.5059 (OUTLIER) cc_final: 0.4382 (mt) REVERT: I 217 LYS cc_start: 0.7544 (mtpt) cc_final: 0.7204 (mttm) REVERT: I 272 GLU cc_start: 0.8131 (pt0) cc_final: 0.7796 (mp0) REVERT: I 311 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8555 (tt) REVERT: J 43 ASP cc_start: 0.7953 (m-30) cc_final: 0.7686 (m-30) REVERT: J 308 GLU cc_start: 0.5983 (tm-30) cc_final: 0.5711 (tm-30) REVERT: J 323 MET cc_start: 0.4446 (tpp) cc_final: 0.4175 (tpp) outliers start: 112 outliers final: 79 residues processed: 365 average time/residue: 0.1639 time to fit residues: 98.4918 Evaluate side-chains 344 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 258 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 226 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN H 148 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.149361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114729 restraints weight = 44615.626| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.56 r_work: 0.3090 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29816 Z= 0.184 Angle : 0.830 13.683 40742 Z= 0.409 Chirality : 0.055 0.445 4503 Planarity : 0.005 0.075 5002 Dihedral : 13.163 165.059 4447 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.56 % Allowed : 15.62 % Favored : 83.82 % Rotamer: Outliers : 3.67 % Allowed : 17.95 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 2.42 % Twisted General : 1.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.14), residues: 3400 helix: -0.76 (0.17), residues: 926 sheet: -0.53 (0.23), residues: 493 loop : -3.32 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 291 TYR 0.018 0.002 TYR I 9 PHE 0.022 0.001 PHE I 238 TRP 0.023 0.001 TRP A 24 HIS 0.013 0.001 HIS G 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (29814) covalent geometry : angle 0.83049 / 0.41 (40742) hydrogen bonds : bond 0.03522 / 2.34 ( 753) hydrogen bonds : angle 5.09248 / 3.50 ( 2089) Misc. bond : bond 0.00440 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 274 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8089 (tp40) cc_final: 0.7824 (tp-100) REVERT: A 307 PHE cc_start: 0.8085 (m-10) cc_final: 0.7821 (m-10) REVERT: B 6 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8255 (t0) REVERT: B 138 ASN cc_start: 0.8467 (p0) cc_final: 0.7910 (p0) REVERT: C 252 ASP cc_start: 0.8071 (m-30) cc_final: 0.7834 (t0) REVERT: C 347 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: D 71 HIS cc_start: 0.7642 (m-70) cc_final: 0.7391 (t-170) REVERT: E 252 ASP cc_start: 0.8568 (t0) cc_final: 0.8215 (t0) REVERT: F 43 MET cc_start: 0.6050 (mpp) cc_final: 0.5472 (mpp) REVERT: F 135 ASN cc_start: 0.8554 (p0) cc_final: 0.8216 (p0) REVERT: F 263 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8385 (tptt) REVERT: G 21 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.6841 (ptm160) REVERT: G 622 TYR cc_start: 0.7787 (p90) cc_final: 0.7532 (p90) REVERT: H 16 ASN cc_start: 0.8479 (t0) cc_final: 0.8221 (t0) REVERT: H 63 LYS cc_start: 0.7726 (tmmt) cc_final: 0.7325 (tptm) REVERT: H 77 GLN cc_start: 0.7293 (tp-100) cc_final: 0.7014 (mt0) REVERT: H 88 ASN cc_start: 0.7409 (m-40) cc_final: 0.6770 (t0) REVERT: H 164 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6685 (mtp180) REVERT: H 194 GLN cc_start: 0.7574 (pp30) cc_final: 0.7134 (tm-30) REVERT: I 1 MET cc_start: 0.2104 (tpp) cc_final: 0.0021 (tpt) REVERT: I 3 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4504 (mt) REVERT: I 217 LYS cc_start: 0.7462 (mtpt) cc_final: 0.7148 (mttm) REVERT: I 272 GLU cc_start: 0.8107 (pt0) cc_final: 0.7775 (mp0) REVERT: I 311 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8530 (tt) REVERT: J 43 ASP cc_start: 0.7915 (m-30) cc_final: 0.7627 (m-30) REVERT: J 308 GLU cc_start: 0.6050 (tm-30) cc_final: 0.5760 (tm-30) outliers start: 112 outliers final: 79 residues processed: 369 average time/residue: 0.1669 time to fit residues: 102.4999 Evaluate side-chains 352 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 266 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 494 ASP Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 238 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 334 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 321 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 325 optimal weight: 10.0000 chunk 236 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 270 optimal weight: 40.0000 chunk 266 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 GLN ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS I 151 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112760 restraints weight = 44537.317| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.79 r_work: 0.3039 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29816 Z= 0.227 Angle : 0.870 13.931 40742 Z= 0.428 Chirality : 0.057 0.514 4503 Planarity : 0.005 0.074 5002 Dihedral : 13.231 164.017 4447 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.59 % Allowed : 16.38 % Favored : 83.03 % Rotamer: Outliers : 3.51 % Allowed : 18.34 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 1.01 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.14), residues: 3400 helix: -0.84 (0.17), residues: 932 sheet: -0.52 (0.23), residues: 492 loop : -3.33 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 291 TYR 0.023 0.002 TYR G 197 PHE 0.029 0.002 PHE I 238 TRP 0.023 0.002 TRP J 142 HIS 0.011 0.001 HIS G 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (29814) covalent geometry : angle 0.87048 / 0.43 (40742) hydrogen bonds : bond 0.03830 / 2.54 ( 753) hydrogen bonds : angle 5.16875 / 3.54 ( 2089) Misc. bond : bond 0.00407 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 270 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8107 (tp40) cc_final: 0.7747 (tp-100) REVERT: A 307 PHE cc_start: 0.8119 (m-10) cc_final: 0.7888 (m-10) REVERT: B 6 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8241 (t0) REVERT: B 138 ASN cc_start: 0.8571 (p0) cc_final: 0.8274 (p0) REVERT: C 252 ASP cc_start: 0.8080 (m-30) cc_final: 0.7843 (t0) REVERT: C 347 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: D 71 HIS cc_start: 0.7719 (m-70) cc_final: 0.7439 (t-170) REVERT: E 252 ASP cc_start: 0.8626 (t0) cc_final: 0.8271 (t0) REVERT: F 43 MET cc_start: 0.6168 (mpp) cc_final: 0.5703 (mpp) REVERT: F 263 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8476 (tptt) REVERT: G 21 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6906 (ptm160) REVERT: G 44 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.8036 (p) REVERT: G 622 TYR cc_start: 0.7928 (p90) cc_final: 0.7645 (p90) REVERT: H 16 ASN cc_start: 0.8491 (t0) cc_final: 0.8183 (t0) REVERT: H 63 LYS cc_start: 0.7795 (tmmt) cc_final: 0.7386 (tptm) REVERT: H 88 ASN cc_start: 0.7441 (m-40) cc_final: 0.6777 (t0) REVERT: H 164 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6752 (mtp180) REVERT: H 176 GLU cc_start: 0.5879 (OUTLIER) cc_final: 0.3806 (tm-30) REVERT: H 194 GLN cc_start: 0.7583 (pp30) cc_final: 0.7120 (pp30) REVERT: I 1 MET cc_start: 0.2158 (tpp) cc_final: 0.0132 (tpt) REVERT: I 3 LEU cc_start: 0.5268 (OUTLIER) cc_final: 0.4582 (mt) REVERT: I 217 LYS cc_start: 0.7446 (mtpt) cc_final: 0.7086 (tmtt) REVERT: I 272 GLU cc_start: 0.8152 (pt0) cc_final: 0.7804 (mp0) REVERT: I 311 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8639 (tt) REVERT: J 308 GLU cc_start: 0.6081 (tm-30) cc_final: 0.5827 (tm-30) REVERT: J 323 MET cc_start: 0.4353 (tpp) cc_final: 0.3997 (tpp) outliers start: 107 outliers final: 79 residues processed: 360 average time/residue: 0.1639 time to fit residues: 97.3811 Evaluate side-chains 347 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 259 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 238 PHE Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 311 LEU Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 17 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 chunk 287 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS I 151 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.149857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116436 restraints weight = 44331.203| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.70 r_work: 0.3091 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29816 Z= 0.154 Angle : 0.815 14.865 40742 Z= 0.401 Chirality : 0.053 0.423 4503 Planarity : 0.005 0.074 5002 Dihedral : 13.040 166.395 4447 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.97 % Favored : 84.56 % Rotamer: Outliers : 2.76 % Allowed : 19.13 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 0.95 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.14), residues: 3400 helix: -0.74 (0.17), residues: 934 sheet: -0.57 (0.22), residues: 521 loop : -3.24 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 291 TYR 0.019 0.001 TYR I 390 PHE 0.024 0.001 PHE I 238 TRP 0.025 0.001 TRP A 24 HIS 0.012 0.001 HIS G 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (29814) covalent geometry : angle 0.81484 / 0.40 (40742) hydrogen bonds : bond 0.03319 / 2.20 ( 753) hydrogen bonds : angle 5.07761 / 3.49 ( 2089) Misc. bond : bond 0.00387 / 0.19 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6800 Ramachandran restraints generated. 3400 Oldfield, 0 Emsley, 3400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 285 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8097 (tp40) cc_final: 0.7711 (tp-100) REVERT: A 307 PHE cc_start: 0.8053 (m-10) cc_final: 0.7833 (m-10) REVERT: A 320 LEU cc_start: 0.7155 (tp) cc_final: 0.6612 (pp) REVERT: B 6 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8194 (t0) REVERT: B 138 ASN cc_start: 0.8410 (p0) cc_final: 0.7866 (t0) REVERT: C 252 ASP cc_start: 0.8089 (m-30) cc_final: 0.7837 (t0) REVERT: C 347 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: E 252 ASP cc_start: 0.8594 (t0) cc_final: 0.8235 (t0) REVERT: F 43 MET cc_start: 0.6055 (mpp) cc_final: 0.5664 (mpp) REVERT: F 135 ASN cc_start: 0.8427 (p0) cc_final: 0.8132 (p0) REVERT: F 263 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8333 (tptt) REVERT: G 588 HIS cc_start: 0.7499 (t70) cc_final: 0.7220 (t70) REVERT: G 622 TYR cc_start: 0.7856 (p90) cc_final: 0.7637 (p90) REVERT: H 16 ASN cc_start: 0.8475 (t0) cc_final: 0.8089 (t0) REVERT: H 63 LYS cc_start: 0.7813 (tmmt) cc_final: 0.7408 (tptm) REVERT: H 77 GLN cc_start: 0.6954 (mt0) cc_final: 0.6491 (tp-100) REVERT: H 88 ASN cc_start: 0.7343 (m-40) cc_final: 0.6752 (t0) REVERT: H 164 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6673 (mtp180) REVERT: H 169 MET cc_start: 0.7586 (ttp) cc_final: 0.7356 (tmm) REVERT: H 176 GLU cc_start: 0.5916 (OUTLIER) cc_final: 0.3643 (tm-30) REVERT: H 194 GLN cc_start: 0.7337 (pp30) cc_final: 0.6988 (tm-30) REVERT: I 1 MET cc_start: 0.2113 (tpp) cc_final: 0.0152 (tpt) REVERT: I 3 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.4518 (mt) REVERT: I 217 LYS cc_start: 0.7405 (mtpt) cc_final: 0.7073 (tmtt) REVERT: I 272 GLU cc_start: 0.8129 (pt0) cc_final: 0.7784 (mp0) REVERT: I 333 ASN cc_start: 0.7846 (t0) cc_final: 0.7445 (p0) REVERT: J 43 ASP cc_start: 0.7996 (m-30) cc_final: 0.7721 (m-30) REVERT: J 308 GLU cc_start: 0.6013 (tm-30) cc_final: 0.5751 (tm-30) REVERT: J 323 MET cc_start: 0.4284 (tpp) cc_final: 0.3919 (tpp) outliers start: 84 outliers final: 67 residues processed: 352 average time/residue: 0.1798 time to fit residues: 104.9290 Evaluate side-chains 340 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 267 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 164 ARG Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 238 PHE Chi-restraints excluded: chain I residue 240 PHE Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 339 ILE Chi-restraints excluded: chain J residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 209 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 312 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 GLN ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 493 GLN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS I 151 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 HIS ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113539 restraints weight = 44779.587| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.84 r_work: 0.3036 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29816 Z= 0.230 Angle : 0.873 14.776 40742 Z= 0.430 Chirality : 0.058 0.497 4503 Planarity : 0.006 0.072 5002 Dihedral : 13.148 164.453 4447 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.50 % Allowed : 16.62 % Favored : 82.88 % Rotamer: Outliers : 2.92 % Allowed : 19.06 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 0.89 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.14), residues: 3400 helix: -0.84 (0.17), residues: 935 sheet: -0.45 (0.23), residues: 503 loop : -3.29 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 291 TYR 0.022 0.002 TYR E 275 PHE 0.026 0.002 PHE I 238 TRP 0.029 0.002 TRP J 142 HIS 0.029 0.001 HIS J 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (29814) covalent geometry : angle 0.87256 / 0.43 (40742) hydrogen bonds : bond 0.03847 / 2.54 ( 753) hydrogen bonds : angle 5.12481 / 3.52 ( 2089) Misc. bond : bond 0.00397 / 0.19 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6040.80 seconds wall clock time: 104 minutes 46.81 seconds (6286.81 seconds total)