Starting phenix.real_space_refine on Tue Jun 24 23:00:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pif_20349/06_2025/6pif_20349.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pif_20349/06_2025/6pif_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pif_20349/06_2025/6pif_20349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pif_20349/06_2025/6pif_20349.map" model { file = "/net/cci-nas-00/data/ceres_data/6pif_20349/06_2025/6pif_20349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pif_20349/06_2025/6pif_20349.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 14, 'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna2p': 23, 'rna3p': 36} Time building chain proxies: 16.62, per 1000 atoms: 0.57 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: 6.55 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 9.28 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: 9.05 Time building geometry restraints manager: 7.82 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: 29066 1.84 - 3.69: 9943 3.69 - 5.53: 1612 5.53 - 7.37: 111 7.37 - 9.22: 10 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 - 35.78: 17266 35.78 - 71.56: 509 71.56 - 107.34: 42 107.34 - 143.12: 4 143.12 - 178.90: 3 Dihedral angle restraints: 17824 sinusoidal: 7710 harmonic: 10114 Sorted by residual: dihedral pdb=" CA LYS G 49 " pdb=" C LYS G 49 " pdb=" N THR G 50 " pdb=" CA THR G 50 " ideal model delta harmonic sigma weight residual 180.00 45.09 134.91 0 5.00e+00 4.00e-02 7.28e+02 dihedral pdb=" CA LEU G 57 " pdb=" C LEU G 57 " pdb=" N ASP G 58 " pdb=" CA ASP G 58 " ideal model delta harmonic sigma weight residual 180.00 68.17 111.83 0 5.00e+00 4.00e-02 5.00e+02 dihedral pdb=" CA ASP G 58 " pdb=" C ASP G 58 " pdb=" N ARG G 59 " pdb=" CA ARG G 59 " ideal model delta harmonic sigma weight residual -180.00 -73.00 -107.00 0 5.00e+00 4.00e-02 4.58e+02 ... (remaining 17821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2064 0.057 - 0.115: 1611 0.115 - 0.172: 671 0.172 - 0.230: 148 0.230 - 0.287: 9 Chirality restraints: 4503 Sorted by residual: chirality pdb=" C1' U 1 21 " pdb=" O4' U 1 21 " pdb=" C2' U 1 21 " pdb=" N1 U 1 21 " both_signs ideal model delta sigma weight residual False 2.47 2.18 0.29 2.00e-01 2.50e+01 2.06e+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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.130 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 66.130 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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= 1.064 Angle : 1.740 9.218 40742 Z= 1.230 Chirality : 0.085 0.287 4503 Planarity : 0.004 0.120 5002 Dihedral : 17.072 178.905 11252 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 6.99 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.002 TRP A 24 HIS 0.009 0.002 HIS E 299 PHE 0.019 0.002 PHE I 144 TYR 0.025 0.002 TYR I 101 ARG 0.018 0.001 ARG D 178 Details of bonding type rmsd hydrogen bonds : bond 0.21182 ( 753) hydrogen bonds : angle 8.79432 ( 2089) covalent geometry : bond 0.01367 (29814) covalent geometry : angle 1.74020 (40742) Misc. bond : bond 0.28916 ( 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 : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.7325 (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: 0.6851 (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: 0.1984 (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: 0.7751 (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: 0.4531 time to fit residues: 475.3643 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 : 2.973 ------------------------------------------------------------------------------- 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 291 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 139 optimal weight: 0.2980 chunk 270 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 174 ASN A 218 ASN B 135 ASN B 183 ASN B 311 GLN B 312 GLN B 315 HIS C 104 ASN C 174 ASN C 311 GLN C 323 ASN D 174 ASN D 183 ASN 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 F 349 HIS G 180 GLN G 196 ASN G 227 GLN G 392 ASN G 444 GLN G 490 HIS H 73 HIS H 88 ASN H 132 GLN I 80 GLN I 84 ASN I 265 HIS I 386 ASN J 95 ASN ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.153759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.118539 restraints weight = 44197.997| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.88 r_work: 0.3110 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29816 Z= 0.167 Angle : 0.831 12.065 40742 Z= 0.439 Chirality : 0.048 0.322 4503 Planarity : 0.005 0.091 5002 Dihedral : 15.959 175.727 4722 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 1.09 % Allowed : 13.94 % Favored : 84.97 % Rotamer: Outliers : 2.85 % Allowed : 11.32 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 5.45 % Twisted General : 1.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.13), residues: 3400 helix: -1.50 (0.16), residues: 903 sheet: -1.03 (0.23), residues: 463 loop : -3.77 (0.11), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 24 HIS 0.010 0.001 HIS G 490 PHE 0.020 0.002 PHE G 433 TYR 0.026 0.002 TYR I 101 ARG 0.008 0.000 ARG I 5 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 753) hydrogen bonds : angle 5.77664 ( 2089) covalent geometry : bond 0.00355 (29814) covalent geometry : angle 0.83148 (40742) Misc. bond : bond 0.00415 ( 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 448 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 361 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 VAL cc_start: 0.6652 (OUTLIER) cc_final: 0.6428 (m) REVERT: A 114 GLN cc_start: 0.8050 (tp40) cc_final: 0.7716 (tp-100) REVERT: A 202 ASP cc_start: 0.6780 (m-30) cc_final: 0.6578 (t0) REVERT: B 17 ASP cc_start: 0.8442 (p0) cc_final: 0.8149 (p0) REVERT: B 185 LYS cc_start: 0.5331 (pttm) cc_final: 0.5048 (mtmt) REVERT: C 252 ASP cc_start: 0.8195 (m-30) cc_final: 0.7843 (t0) REVERT: D 71 HIS cc_start: 0.7605 (m-70) cc_final: 0.7245 (t-170) REVERT: D 86 GLU cc_start: 0.8229 (tt0) cc_final: 0.8018 (tt0) REVERT: F 188 SER cc_start: 0.8665 (m) cc_final: 0.8440 (p) REVERT: F 210 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7975 (ttm170) REVERT: F 263 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8464 (tttp) REVERT: G 19 LEU cc_start: 0.8332 (tp) cc_final: 0.7739 (tp) REVERT: G 23 PHE cc_start: 0.8170 (m-80) cc_final: 0.7821 (m-80) REVERT: G 190 ASN cc_start: 0.7584 (t0) cc_final: 0.7080 (m-40) REVERT: H 16 ASN cc_start: 0.8444 (t0) cc_final: 0.8236 (t0) REVERT: H 29 HIS cc_start: 0.7705 (t70) cc_final: 0.7472 (t-90) REVERT: H 78 MET cc_start: 0.7603 (tpp) cc_final: 0.7303 (tpp) REVERT: H 127 LEU cc_start: 0.5829 (mm) cc_final: 0.5442 (pp) REVERT: H 160 ASN cc_start: 0.7418 (m-40) cc_final: 0.7136 (m110) REVERT: I 3 LEU cc_start: 0.4872 (tp) cc_final: 0.3775 (mt) REVERT: I 66 ASN cc_start: 0.6081 (m-40) cc_final: 0.5105 (t0) REVERT: I 84 ASN cc_start: 0.4997 (OUTLIER) cc_final: 0.4561 (t0) REVERT: I 198 CYS cc_start: 0.6317 (OUTLIER) cc_final: 0.5683 (t) REVERT: I 217 LYS cc_start: 0.7264 (mtpt) cc_final: 0.6950 (mttp) REVERT: I 272 GLU cc_start: 0.8110 (pt0) cc_final: 0.7713 (mp0) REVERT: I 386 ASN cc_start: 0.8280 (t0) cc_final: 0.8052 (t0) REVERT: J 43 ASP cc_start: 0.7899 (m-30) cc_final: 0.7412 (m-30) REVERT: J 47 ASN cc_start: 0.8241 (p0) cc_final: 0.7914 (m-40) REVERT: J 85 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7871 (mp0) REVERT: J 108 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7361 (m) REVERT: J 153 HIS cc_start: 0.5799 (OUTLIER) cc_final: 0.5587 (p90) REVERT: J 323 MET cc_start: 0.4813 (tpp) cc_final: 0.4590 (tpp) REVERT: J 375 LEU cc_start: 0.7249 (tp) cc_final: 0.6894 (tt) outliers start: 87 outliers final: 46 residues processed: 427 average time/residue: 0.4326 time to fit residues: 295.1800 Evaluate side-chains 324 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 3.479 ------------------------------------------------------------------------------- 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 79 VAL 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 102 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 331 MET 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 272 optimal weight: 8.9990 chunk 69 optimal weight: 0.1980 chunk 230 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 258 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 319 optimal weight: 0.9990 chunk 249 optimal weight: 0.1980 chunk 341 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 311 GLN ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS E 214 HIS E 241 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 315 HIS G 384 ASN G 548 ASN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 HIS I 31 HIS I 151 HIS ** J 46 HIS ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119168 restraints weight = 44299.846| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.80 r_work: 0.3100 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29816 Z= 0.148 Angle : 0.771 11.193 40742 Z= 0.401 Chirality : 0.046 0.269 4503 Planarity : 0.005 0.064 5002 Dihedral : 15.395 175.509 4677 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.79 % Allowed : 14.88 % Favored : 84.32 % Rotamer: Outliers : 3.38 % Allowed : 13.12 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 6.06 % Twisted General : 1.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.13), residues: 3400 helix: -1.11 (0.17), residues: 899 sheet: -0.88 (0.23), residues: 473 loop : -3.63 (0.11), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 24 HIS 0.018 0.001 HIS H 73 PHE 0.020 0.001 PHE I 240 TYR 0.018 0.001 TYR I 390 ARG 0.005 0.000 ARG G 59 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 753) hydrogen bonds : angle 5.32083 ( 2089) covalent geometry : bond 0.00326 (29814) covalent geometry : angle 0.77105 (40742) Misc. bond : bond 0.00191 ( 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 432 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 329 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8081 (tp40) cc_final: 0.7749 (tp-100) REVERT: A 202 ASP cc_start: 0.6759 (m-30) cc_final: 0.6542 (t0) REVERT: A 293 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6701 (p0) REVERT: A 294 VAL cc_start: 0.7126 (OUTLIER) cc_final: 0.6909 (p) REVERT: A 307 PHE cc_start: 0.8088 (m-10) cc_final: 0.7851 (m-10) REVERT: B 17 ASP cc_start: 0.8465 (p0) cc_final: 0.8102 (p0) REVERT: B 138 ASN cc_start: 0.8339 (p0) cc_final: 0.7993 (p0) REVERT: C 118 LEU cc_start: 0.9056 (mm) cc_final: 0.8831 (mp) REVERT: C 252 ASP cc_start: 0.8199 (m-30) cc_final: 0.7879 (t0) REVERT: D 71 HIS cc_start: 0.7618 (m-70) cc_final: 0.7270 (t-170) REVERT: E 252 ASP cc_start: 0.8503 (t0) cc_final: 0.8081 (t0) REVERT: F 188 SER cc_start: 0.8635 (m) cc_final: 0.8422 (p) REVERT: F 263 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8576 (tttp) REVERT: G 5 LYS cc_start: 0.6393 (mptt) cc_final: 0.6128 (tmtt) REVERT: G 19 LEU cc_start: 0.8347 (tp) cc_final: 0.8140 (tp) REVERT: G 23 PHE cc_start: 0.8143 (m-80) cc_final: 0.7735 (m-80) REVERT: G 231 ASP cc_start: 0.7493 (m-30) cc_final: 0.6918 (p0) REVERT: G 588 HIS cc_start: 0.7368 (t70) cc_final: 0.7164 (t70) REVERT: H 16 ASN cc_start: 0.8508 (t0) cc_final: 0.8090 (t0) REVERT: H 29 HIS cc_start: 0.7882 (t70) cc_final: 0.7663 (t-90) REVERT: H 81 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8603 (pp) REVERT: H 88 ASN cc_start: 0.7339 (m-40) cc_final: 0.6708 (t0) REVERT: H 93 PRO cc_start: 0.5643 (Cg_exo) cc_final: 0.5428 (Cg_endo) REVERT: H 127 LEU cc_start: 0.5800 (mm) cc_final: 0.5583 (pp) REVERT: H 181 PHE cc_start: 0.4678 (OUTLIER) cc_final: 0.4206 (p90) REVERT: H 194 GLN cc_start: 0.7323 (pp30) cc_final: 0.7093 (pp30) REVERT: H 195 PRO cc_start: 0.8303 (Cg_exo) cc_final: 0.7991 (Cg_endo) REVERT: H 197 PRO cc_start: 0.8715 (Cg_endo) cc_final: 0.8200 (Cg_exo) REVERT: I 1 MET cc_start: 0.2016 (tpt) cc_final: 0.1805 (tpp) REVERT: I 3 LEU cc_start: 0.5036 (tp) cc_final: 0.3746 (mt) REVERT: I 198 CYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6297 (t) REVERT: I 217 LYS cc_start: 0.7310 (mtpt) cc_final: 0.7056 (mttp) REVERT: I 272 GLU cc_start: 0.7985 (pt0) cc_final: 0.7660 (mp0) REVERT: J 39 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8212 (mtm110) REVERT: J 43 ASP cc_start: 0.7935 (m-30) cc_final: 0.7497 (m-30) REVERT: J 47 ASN cc_start: 0.8101 (p0) cc_final: 0.7777 (m110) REVERT: J 108 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7685 (m) REVERT: J 133 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6474 (mtt90) REVERT: J 153 HIS cc_start: 0.5933 (OUTLIER) cc_final: 0.5721 (p90) REVERT: J 158 ILE cc_start: 0.7181 (pt) cc_final: 0.6816 (mp) REVERT: J 163 CYS cc_start: 0.6131 (m) cc_final: 0.5669 (m) REVERT: J 308 GLU cc_start: 0.6257 (tm-30) cc_final: 0.6034 (tm-30) REVERT: J 323 MET cc_start: 0.4993 (tpp) cc_final: 0.4748 (tpp) REVERT: J 324 ASN cc_start: 0.5212 (t0) cc_final: 0.4901 (t0) outliers start: 103 outliers final: 56 residues processed: 413 average time/residue: 0.3965 time to fit residues: 266.1691 Evaluate side-chains 349 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 293 ASP Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 PHE 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 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 241 GLN Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 294 VAL 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 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 517 LYS Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain H residue 46 LEU 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 181 PHE Chi-restraints excluded: chain H residue 191 ASN 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 241 VAL Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 331 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 281 optimal weight: 20.0000 chunk 93 optimal weight: 0.4980 chunk 293 optimal weight: 9.9990 chunk 117 optimal weight: 0.6980 chunk 285 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 242 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 ASN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN H 73 HIS H 132 GLN H 148 HIS I 84 ASN I 154 ASN ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 HIS ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.151647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117573 restraints weight = 44382.782| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.79 r_work: 0.3081 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29816 Z= 0.155 Angle : 0.758 11.082 40742 Z= 0.393 Chirality : 0.046 0.247 4503 Planarity : 0.005 0.061 5002 Dihedral : 15.037 176.023 4676 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.38 % Favored : 84.91 % Rotamer: Outliers : 3.67 % Allowed : 14.53 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.64 % Twisted General : 1.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.13), residues: 3400 helix: -0.96 (0.17), residues: 925 sheet: -0.98 (0.22), residues: 521 loop : -3.52 (0.12), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 24 HIS 0.021 0.001 HIS H 73 PHE 0.015 0.001 PHE F 89 TYR 0.023 0.001 TYR G 197 ARG 0.006 0.000 ARG F 286 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 753) hydrogen bonds : angle 5.13446 ( 2089) covalent geometry : bond 0.00346 (29814) covalent geometry : angle 0.75822 (40742) Misc. bond : bond 0.00650 ( 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 419 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 307 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8033 (tp40) cc_final: 0.7690 (tp-100) REVERT: A 202 ASP cc_start: 0.6762 (m-30) cc_final: 0.6501 (t0) REVERT: A 293 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6926 (p0) REVERT: A 307 PHE cc_start: 0.8063 (m-10) cc_final: 0.7783 (m-10) REVERT: B 17 ASP cc_start: 0.8502 (p0) cc_final: 0.8251 (p0) REVERT: B 138 ASN cc_start: 0.8401 (p0) cc_final: 0.7995 (p0) REVERT: C 118 LEU cc_start: 0.9043 (mm) cc_final: 0.8801 (mp) REVERT: C 252 ASP cc_start: 0.8129 (m-30) cc_final: 0.7849 (t0) REVERT: D 71 HIS cc_start: 0.7702 (m-70) cc_final: 0.7272 (t-170) REVERT: E 252 ASP cc_start: 0.8500 (t0) cc_final: 0.8135 (t0) REVERT: E 333 ASP cc_start: 0.8102 (m-30) cc_final: 0.7868 (m-30) REVERT: F 37 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7326 (mtp180) REVERT: F 188 SER cc_start: 0.8700 (m) cc_final: 0.8495 (p) REVERT: F 263 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8566 (tttp) REVERT: G 5 LYS cc_start: 0.6680 (mptt) cc_final: 0.6444 (tmmt) REVERT: G 19 LEU cc_start: 0.8373 (tp) cc_final: 0.8151 (tp) REVERT: G 23 PHE cc_start: 0.8129 (m-80) cc_final: 0.7833 (m-80) REVERT: G 566 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8598 (m) REVERT: H 16 ASN cc_start: 0.8554 (t0) cc_final: 0.8306 (t0) REVERT: H 29 HIS cc_start: 0.8033 (t70) cc_final: 0.7831 (t-90) REVERT: H 77 GLN cc_start: 0.7430 (tp-100) cc_final: 0.7165 (mt0) REVERT: H 78 MET cc_start: 0.7648 (tpp) cc_final: 0.7314 (tpp) REVERT: H 88 ASN cc_start: 0.7245 (m-40) cc_final: 0.6688 (t0) REVERT: H 93 PRO cc_start: 0.6014 (Cg_exo) cc_final: 0.5802 (Cg_endo) REVERT: H 105 GLN cc_start: 0.8681 (tt0) cc_final: 0.8453 (tt0) REVERT: H 169 MET cc_start: 0.8122 (tmm) cc_final: 0.7886 (tmm) REVERT: H 181 PHE cc_start: 0.4243 (OUTLIER) cc_final: 0.3932 (p90) REVERT: H 190 GLU cc_start: 0.5683 (pt0) cc_final: 0.5340 (pt0) REVERT: H 194 GLN cc_start: 0.7342 (pp30) cc_final: 0.7123 (pp30) REVERT: H 195 PRO cc_start: 0.8312 (Cg_exo) cc_final: 0.8026 (Cg_endo) REVERT: I 3 LEU cc_start: 0.5128 (tp) cc_final: 0.3977 (mt) REVERT: I 84 ASN cc_start: 0.4543 (OUTLIER) cc_final: 0.4330 (t0) REVERT: I 217 LYS cc_start: 0.7449 (mtpt) cc_final: 0.7203 (mttp) REVERT: I 272 GLU cc_start: 0.7953 (pt0) cc_final: 0.7705 (mp0) REVERT: J 43 ASP cc_start: 0.7905 (m-30) cc_final: 0.7605 (m-30) REVERT: J 47 ASN cc_start: 0.8169 (p0) cc_final: 0.7839 (m110) REVERT: J 133 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.6265 (mmt180) REVERT: J 308 GLU cc_start: 0.6201 (tm-30) cc_final: 0.5908 (tm-30) REVERT: J 323 MET cc_start: 0.5327 (tpp) cc_final: 0.5096 (tpp) outliers start: 112 outliers final: 62 residues processed: 392 average time/residue: 0.3823 time to fit residues: 242.2492 Evaluate side-chains 352 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 283 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 293 ASP 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 97 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 226 VAL 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 331 ILE 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 196 THR 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 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 F residue 315 HIS 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 229 LEU Chi-restraints excluded: chain G residue 392 ASN 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 G residue 566 SER Chi-restraints excluded: chain G residue 572 LEU Chi-restraints excluded: chain G residue 600 SER Chi-restraints excluded: chain G residue 623 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 52 VAL 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 181 PHE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 127 CYS Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 331 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 196 optimal weight: 6.9990 chunk 183 optimal weight: 0.0970 chunk 71 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 323 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 287 optimal weight: 10.0000 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 110 GLN B 55 GLN B 104 ASN 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 ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS G 196 ASN ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 ASN G 493 GLN ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 HIS ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.144981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.109746 restraints weight = 44537.070| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.96 r_work: 0.2977 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 29816 Z= 0.316 Angle : 0.875 20.765 40742 Z= 0.455 Chirality : 0.051 0.279 4503 Planarity : 0.006 0.060 5002 Dihedral : 15.127 178.342 4669 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.79 % Allowed : 16.21 % Favored : 83.00 % Rotamer: Outliers : 4.00 % Allowed : 15.16 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 1.82 % Twisted General : 1.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.13), residues: 3400 helix: -1.10 (0.17), residues: 939 sheet: -0.62 (0.23), residues: 480 loop : -3.54 (0.12), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 142 HIS 0.038 0.002 HIS F 315 PHE 0.026 0.002 PHE G 613 TYR 0.028 0.002 TYR E 275 ARG 0.008 0.001 ARG F 283 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 753) hydrogen bonds : angle 5.28357 ( 2089) covalent geometry : bond 0.00747 (29814) covalent geometry : angle 0.87479 (40742) Misc. bond : bond 0.00576 ( 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 406 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 284 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.7096 (m-30) cc_final: 0.6500 (t0) REVERT: A 307 PHE cc_start: 0.8376 (m-10) cc_final: 0.8037 (m-10) REVERT: C 252 ASP cc_start: 0.8151 (m-30) cc_final: 0.7878 (t0) REVERT: C 347 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8793 (m-80) REVERT: D 71 HIS cc_start: 0.7835 (m-70) cc_final: 0.7446 (t-170) REVERT: E 241 GLN cc_start: 0.6457 (OUTLIER) cc_final: 0.5465 (pm20) REVERT: E 252 ASP cc_start: 0.8633 (t0) cc_final: 0.8257 (t0) REVERT: E 333 ASP cc_start: 0.8283 (m-30) cc_final: 0.8023 (m-30) REVERT: F 188 SER cc_start: 0.8910 (m) cc_final: 0.8691 (p) REVERT: F 294 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8650 (t) REVERT: G 5 LYS cc_start: 0.6680 (mptt) cc_final: 0.6267 (tmtt) REVERT: G 23 PHE cc_start: 0.8082 (m-80) cc_final: 0.7766 (m-80) REVERT: H 16 ASN cc_start: 0.8660 (t0) cc_final: 0.8375 (t0) REVERT: H 40 ILE cc_start: 0.8014 (mm) cc_final: 0.7559 (mt) REVERT: H 77 GLN cc_start: 0.7586 (tp-100) cc_final: 0.7210 (mt0) REVERT: H 78 MET cc_start: 0.7488 (tpp) cc_final: 0.7164 (tpp) REVERT: H 88 ASN cc_start: 0.7339 (m-40) cc_final: 0.6693 (t0) REVERT: H 105 GLN cc_start: 0.8804 (tt0) cc_final: 0.8531 (tt0) REVERT: H 107 ILE cc_start: 0.8492 (mm) cc_final: 0.8290 (mt) REVERT: H 176 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5587 (pt0) REVERT: H 181 PHE cc_start: 0.4537 (OUTLIER) cc_final: 0.4123 (p90) REVERT: H 194 GLN cc_start: 0.7410 (pp30) cc_final: 0.7205 (pp30) REVERT: I 84 ASN cc_start: 0.5134 (OUTLIER) cc_final: 0.4887 (t0) REVERT: I 110 ARG cc_start: 0.5767 (tpm170) cc_final: 0.4647 (tpt90) REVERT: I 217 LYS cc_start: 0.7590 (mtpt) cc_final: 0.7282 (mttp) REVERT: I 272 GLU cc_start: 0.8239 (pt0) cc_final: 0.7827 (mp0) REVERT: I 326 LEU cc_start: 0.8455 (mt) cc_final: 0.8254 (mp) REVERT: J 308 GLU cc_start: 0.6272 (tm-30) cc_final: 0.5925 (tm-30) REVERT: J 387 ARG cc_start: 0.6574 (tmt170) cc_final: 0.6310 (ptm-80) outliers start: 122 outliers final: 73 residues processed: 386 average time/residue: 0.3751 time to fit residues: 235.3679 Evaluate side-chains 334 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 255 time to evaluate : 2.935 ------------------------------------------------------------------------------- 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 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 331 ILE Chi-restraints excluded: chain B residue 347 PHE 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 C residue 325 THR 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 331 ILE Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 43 MET 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 209 VAL Chi-restraints excluded: chain E residue 241 GLN 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 38 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 294 VAL Chi-restraints excluded: chain G residue 14 ASP 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 229 LEU Chi-restraints excluded: chain G residue 426 ILE Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain G residue 480 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 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 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 176 GLU 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 137 TYR Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 268 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain J residue 102 SER Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 331 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 327 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 319 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 325 optimal weight: 7.9990 chunk 277 optimal weight: 30.0000 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** 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** F 77 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 HIS G 138 ASN ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 HIS I 84 ASN ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 202 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.145895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110721 restraints weight = 44474.050| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.95 r_work: 0.3004 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 29816 Z= 0.240 Angle : 0.822 15.778 40742 Z= 0.424 Chirality : 0.049 0.412 4503 Planarity : 0.006 0.069 5002 Dihedral : 15.044 178.738 4663 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.71 % Allowed : 15.41 % Favored : 83.88 % Rotamer: Outliers : 3.64 % Allowed : 16.34 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 1.82 % Twisted General : 1.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.13), residues: 3400 helix: -1.08 (0.17), residues: 932 sheet: -0.72 (0.23), residues: 496 loop : -3.46 (0.12), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 24 HIS 0.013 0.001 HIS F 315 PHE 0.031 0.002 PHE I 238 TYR 0.021 0.002 TYR H 149 ARG 0.005 0.001 ARG F 286 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 753) hydrogen bonds : angle 5.21188 ( 2089) covalent geometry : bond 0.00562 (29814) covalent geometry : angle 0.82197 (40742) Misc. bond : bond 0.00419 ( 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 393 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 282 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7940 (tm-30) REVERT: B 138 ASN cc_start: 0.8672 (p0) cc_final: 0.8145 (p0) REVERT: C 252 ASP cc_start: 0.8127 (m-30) cc_final: 0.7842 (t0) REVERT: C 291 ARG cc_start: 0.7479 (ttt-90) cc_final: 0.7091 (ttp80) REVERT: C 347 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: D 71 HIS cc_start: 0.7829 (m-70) cc_final: 0.7435 (t-170) REVERT: E 252 ASP cc_start: 0.8615 (t0) cc_final: 0.8253 (t0) REVERT: E 333 ASP cc_start: 0.8267 (m-30) cc_final: 0.7999 (m-30) REVERT: F 188 SER cc_start: 0.8885 (m) cc_final: 0.8652 (p) REVERT: G 5 LYS cc_start: 0.6759 (mptt) cc_final: 0.6383 (tmtt) REVERT: G 622 TYR cc_start: 0.8081 (p90) cc_final: 0.7863 (p90) REVERT: H 16 ASN cc_start: 0.8639 (t0) cc_final: 0.8366 (t0) REVERT: H 77 GLN cc_start: 0.7481 (tp-100) cc_final: 0.7161 (mt0) REVERT: H 78 MET cc_start: 0.7391 (tpp) cc_final: 0.7165 (tpp) REVERT: H 88 ASN cc_start: 0.7461 (m-40) cc_final: 0.6811 (t0) REVERT: H 107 ILE cc_start: 0.8569 (mm) cc_final: 0.8365 (mt) REVERT: H 181 PHE cc_start: 0.4529 (OUTLIER) cc_final: 0.4251 (p90) REVERT: I 110 ARG cc_start: 0.5456 (tpm170) cc_final: 0.4400 (tpm170) REVERT: I 113 GLU cc_start: 0.4244 (mt-10) cc_final: 0.3758 (tt0) REVERT: I 272 GLU cc_start: 0.8234 (pt0) cc_final: 0.7833 (mp0) REVERT: J 308 GLU cc_start: 0.6246 (tm-30) cc_final: 0.5918 (tm-30) REVERT: J 323 MET cc_start: 0.4411 (tpp) cc_final: 0.4175 (tpp) REVERT: J 387 ARG cc_start: 0.6484 (tmt170) cc_final: 0.6193 (ptm-80) REVERT: J 390 TYR cc_start: 0.5581 (p90) cc_final: 0.5241 (p90) outliers start: 111 outliers final: 79 residues processed: 375 average time/residue: 0.5034 time to fit residues: 305.7594 Evaluate side-chains 340 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 259 time to evaluate : 3.557 ------------------------------------------------------------------------------- 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 210 ARG Chi-restraints excluded: chain A residue 212 THR 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 331 ILE Chi-restraints excluded: chain B residue 347 PHE 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 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 213 LEU Chi-restraints excluded: chain D residue 226 VAL 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 38 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 294 VAL Chi-restraints excluded: chain F residue 315 HIS Chi-restraints excluded: chain G residue 14 ASP 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 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 G residue 572 LEU 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 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 181 PHE Chi-restraints excluded: chain H residue 191 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 115 PHE 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 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 121 ARG Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 268 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 170 optimal weight: 3.9990 chunk 304 optimal weight: 7.9990 chunk 159 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 283 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 277 optimal weight: 30.0000 chunk 275 optimal weight: 30.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 348 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 138 ASN G 226 HIS ** 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** I 252 HIS ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 HIS ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112168 restraints weight = 44276.061| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.77 r_work: 0.3041 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 29816 Z= 0.163 Angle : 0.770 13.046 40742 Z= 0.396 Chirality : 0.046 0.234 4503 Planarity : 0.005 0.074 5002 Dihedral : 14.887 178.018 4663 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.62 % Allowed : 15.32 % Favored : 84.06 % Rotamer: Outliers : 3.08 % Allowed : 17.68 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 2.42 % Twisted General : 1.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.14), residues: 3400 helix: -0.92 (0.17), residues: 930 sheet: -0.75 (0.22), residues: 508 loop : -3.37 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 24 HIS 0.023 0.001 HIS F 315 PHE 0.031 0.001 PHE I 238 TYR 0.018 0.001 TYR I 390 ARG 0.005 0.000 ARG F 286 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 753) hydrogen bonds : angle 5.09547 ( 2089) covalent geometry : bond 0.00370 (29814) covalent geometry : angle 0.77035 (40742) Misc. bond : bond 0.00253 ( 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: 94 poor density : 289 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 LEU cc_start: 0.7841 (mt) cc_final: 0.7624 (tt) REVERT: B 138 ASN cc_start: 0.8514 (p0) cc_final: 0.7980 (p0) REVERT: C 252 ASP cc_start: 0.8158 (m-30) cc_final: 0.7850 (t0) REVERT: C 291 ARG cc_start: 0.7343 (ttt-90) cc_final: 0.7062 (ttp80) REVERT: C 347 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8515 (m-80) REVERT: D 71 HIS cc_start: 0.7727 (m-70) cc_final: 0.7406 (t-170) REVERT: E 252 ASP cc_start: 0.8567 (t0) cc_final: 0.8207 (t0) REVERT: F 188 SER cc_start: 0.8776 (m) cc_final: 0.8549 (p) REVERT: G 5 LYS cc_start: 0.6734 (mptt) cc_final: 0.6371 (tmtt) REVERT: G 21 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6898 (ptm160) REVERT: G 622 TYR cc_start: 0.7996 (p90) cc_final: 0.7781 (p90) REVERT: H 16 ASN cc_start: 0.8631 (t0) cc_final: 0.8350 (t0) REVERT: H 88 ASN cc_start: 0.7445 (m-40) cc_final: 0.6817 (t0) REVERT: H 105 GLN cc_start: 0.8727 (tt0) cc_final: 0.8411 (tt0) REVERT: H 176 GLU cc_start: 0.5612 (OUTLIER) cc_final: 0.5261 (pt0) REVERT: H 194 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7213 (tm-30) REVERT: I 18 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.5414 (t80) REVERT: I 113 GLU cc_start: 0.3964 (mt-10) cc_final: 0.3615 (tt0) REVERT: I 217 LYS cc_start: 0.7555 (mtpt) cc_final: 0.7210 (mttm) REVERT: I 237 HIS cc_start: 0.7861 (p90) cc_final: 0.7661 (p-80) REVERT: I 272 GLU cc_start: 0.8169 (pt0) cc_final: 0.7806 (mp0) REVERT: J 43 ASP cc_start: 0.8030 (m-30) cc_final: 0.7778 (m-30) REVERT: J 308 GLU cc_start: 0.6263 (tm-30) cc_final: 0.5882 (tm-30) REVERT: J 323 MET cc_start: 0.4180 (tpp) cc_final: 0.3941 (tpp) REVERT: J 387 ARG cc_start: 0.6377 (tmt170) cc_final: 0.6086 (ptm-80) outliers start: 94 outliers final: 68 residues processed: 362 average time/residue: 0.3850 time to fit residues: 226.7480 Evaluate side-chains 344 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 272 time to evaluate : 2.901 ------------------------------------------------------------------------------- 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 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 331 ILE Chi-restraints excluded: chain B residue 347 PHE 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 193 MET Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 325 THR 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 213 LEU Chi-restraints excluded: chain D residue 226 VAL 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 193 MET 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 38 THR Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 123 ILE 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 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 514 ASP Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 557 MET Chi-restraints excluded: chain G residue 572 LEU 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 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 151 SER 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 18 PHE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 198 CYS 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 215 LEU Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 214 optimal weight: 10.0000 chunk 313 optimal weight: 0.2980 chunk 129 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** G 45 ASN G 138 ASN ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS H 72 GLN I 151 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 HIS ** J 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111725 restraints weight = 44564.776| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.84 r_work: 0.3030 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29816 Z= 0.185 Angle : 0.781 13.525 40742 Z= 0.402 Chirality : 0.047 0.314 4503 Planarity : 0.005 0.075 5002 Dihedral : 14.801 178.166 4663 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.62 % Allowed : 15.38 % Favored : 84.00 % Rotamer: Outliers : 3.28 % Allowed : 17.81 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 2.42 % Twisted General : 1.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.14), residues: 3400 helix: -0.90 (0.17), residues: 933 sheet: -0.71 (0.22), residues: 507 loop : -3.33 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 24 HIS 0.008 0.001 HIS G 272 PHE 0.028 0.002 PHE I 238 TYR 0.018 0.002 TYR I 390 ARG 0.004 0.000 ARG G 59 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 753) hydrogen bonds : angle 5.05164 ( 2089) covalent geometry : bond 0.00427 (29814) covalent geometry : angle 0.78140 (40742) Misc. bond : bond 0.00331 ( 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 380 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 280 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.7408 (tpp) cc_final: 0.5608 (tpp) REVERT: B 6 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8289 (t0) REVERT: B 138 ASN cc_start: 0.8495 (p0) cc_final: 0.7944 (p0) REVERT: C 252 ASP cc_start: 0.8140 (m-30) cc_final: 0.7840 (t0) REVERT: C 347 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8589 (m-80) REVERT: D 71 HIS cc_start: 0.7735 (m-70) cc_final: 0.7430 (t-170) REVERT: E 252 ASP cc_start: 0.8558 (t0) cc_final: 0.8198 (t0) REVERT: F 188 SER cc_start: 0.8797 (m) cc_final: 0.8589 (p) REVERT: G 5 LYS cc_start: 0.6675 (mptt) cc_final: 0.6416 (tmtt) REVERT: G 21 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6917 (ptm160) REVERT: H 16 ASN cc_start: 0.8616 (t0) cc_final: 0.8361 (t0) REVERT: H 77 GLN cc_start: 0.7032 (mt0) cc_final: 0.6450 (tp-100) REVERT: H 88 ASN cc_start: 0.7444 (m-40) cc_final: 0.6803 (t0) REVERT: H 93 PRO cc_start: 0.5836 (Cg_exo) cc_final: 0.5595 (Cg_endo) REVERT: H 105 GLN cc_start: 0.8728 (tt0) cc_final: 0.8400 (tt0) REVERT: H 194 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7202 (tm-30) REVERT: I 113 GLU cc_start: 0.3849 (mt-10) cc_final: 0.3445 (tt0) REVERT: I 217 LYS cc_start: 0.7509 (mtpt) cc_final: 0.7170 (mttm) REVERT: I 272 GLU cc_start: 0.8191 (pt0) cc_final: 0.7814 (mp0) REVERT: I 311 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8577 (tt) REVERT: J 43 ASP cc_start: 0.7988 (m-30) cc_final: 0.7735 (m-30) REVERT: J 308 GLU cc_start: 0.6191 (tm-30) cc_final: 0.5783 (tm-30) REVERT: J 323 MET cc_start: 0.4102 (tpp) cc_final: 0.3854 (tpp) REVERT: J 387 ARG cc_start: 0.6327 (tmt170) cc_final: 0.5892 (ptm-80) outliers start: 100 outliers final: 78 residues processed: 362 average time/residue: 0.3817 time to fit residues: 226.3433 Evaluate side-chains 347 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 265 time to evaluate : 2.950 ------------------------------------------------------------------------------- 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 B residue 6 ASN Chi-restraints excluded: chain B residue 17 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 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 213 LEU 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 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 88 SER Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 21 ARG 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 413 THR Chi-restraints excluded: chain G residue 431 SER 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 572 LEU 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 89 THR Chi-restraints excluded: chain H residue 104 CYS Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 147 TYR Chi-restraints excluded: chain I residue 198 CYS 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 151 HIS Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 339 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 337 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 HIS ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.149244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115417 restraints weight = 44396.749| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.68 r_work: 0.3066 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29816 Z= 0.145 Angle : 0.760 14.715 40742 Z= 0.388 Chirality : 0.045 0.293 4503 Planarity : 0.005 0.074 5002 Dihedral : 14.660 177.549 4661 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.56 % Allowed : 15.06 % Favored : 84.38 % Rotamer: Outliers : 2.79 % Allowed : 18.57 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 0.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.14), residues: 3400 helix: -0.75 (0.17), residues: 930 sheet: -0.64 (0.22), residues: 524 loop : -3.24 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 142 HIS 0.013 0.001 HIS J 151 PHE 0.028 0.001 PHE I 238 TYR 0.018 0.001 TYR I 390 ARG 0.006 0.000 ARG J 387 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 753) hydrogen bonds : angle 4.98255 ( 2089) covalent geometry : bond 0.00323 (29814) covalent geometry : angle 0.76015 (40742) Misc. bond : bond 0.00417 ( 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 384 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 299 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.7157 (tpp) cc_final: 0.5577 (tpp) REVERT: B 6 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8227 (t0) REVERT: B 138 ASN cc_start: 0.8353 (p0) cc_final: 0.7877 (t0) REVERT: C 252 ASP cc_start: 0.8190 (m-30) cc_final: 0.7882 (t0) REVERT: C 323 ASN cc_start: 0.6237 (OUTLIER) cc_final: 0.5458 (m-40) REVERT: C 347 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: D 71 HIS cc_start: 0.7775 (m-70) cc_final: 0.7491 (t-170) REVERT: D 106 SER cc_start: 0.8720 (t) cc_final: 0.8474 (t) REVERT: E 252 ASP cc_start: 0.8600 (t0) cc_final: 0.8272 (t0) REVERT: F 43 MET cc_start: 0.6322 (mpp) cc_final: 0.5932 (mpp) REVERT: F 188 SER cc_start: 0.8768 (m) cc_final: 0.8550 (p) REVERT: G 21 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6855 (ptm160) REVERT: G 584 ARG cc_start: 0.7696 (tpp80) cc_final: 0.7333 (tpp80) REVERT: H 16 ASN cc_start: 0.8644 (t0) cc_final: 0.8401 (t0) REVERT: H 77 GLN cc_start: 0.7119 (mt0) cc_final: 0.6600 (tp-100) REVERT: H 88 ASN cc_start: 0.7393 (m-40) cc_final: 0.6764 (t0) REVERT: H 105 GLN cc_start: 0.8719 (tt0) cc_final: 0.8382 (tt0) REVERT: H 194 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7154 (tm-30) REVERT: I 99 MET cc_start: 0.5972 (mtp) cc_final: 0.5663 (mtt) REVERT: I 272 GLU cc_start: 0.8079 (pt0) cc_final: 0.7786 (mp0) REVERT: I 333 ASN cc_start: 0.7775 (t0) cc_final: 0.7439 (p0) REVERT: J 43 ASP cc_start: 0.7971 (m-30) cc_final: 0.7709 (m-30) REVERT: J 308 GLU cc_start: 0.6205 (tm-30) cc_final: 0.5794 (tm-30) REVERT: J 323 MET cc_start: 0.4040 (tpp) cc_final: 0.3796 (tpp) REVERT: J 387 ARG cc_start: 0.6314 (tmt170) cc_final: 0.5989 (ptm-80) outliers start: 85 outliers final: 65 residues processed: 366 average time/residue: 0.3837 time to fit residues: 229.0106 Evaluate side-chains 346 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 277 time to evaluate : 3.363 ------------------------------------------------------------------------------- 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 B residue 6 ASN Chi-restraints excluded: chain B residue 17 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 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 191 VAL 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 213 LEU 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 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 37 ARG Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 21 ARG 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 431 SER Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 572 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 76 VAL 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 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 37 THR 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 198 CYS 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 215 LEU Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 332 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 214 optimal weight: 20.0000 chunk 304 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 328 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** G 101 GLN ** G 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 HIS ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113361 restraints weight = 44649.427| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.94 r_work: 0.3027 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4596 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= 0.184 Angle : 0.777 14.318 40742 Z= 0.399 Chirality : 0.046 0.289 4503 Planarity : 0.005 0.091 5002 Dihedral : 14.630 177.977 4661 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.68 % Favored : 83.82 % Rotamer: Outliers : 2.72 % Allowed : 18.90 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 0.89 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.14), residues: 3400 helix: -0.80 (0.17), residues: 940 sheet: -0.58 (0.22), residues: 519 loop : -3.26 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 142 HIS 0.022 0.001 HIS J 153 PHE 0.026 0.002 PHE I 238 TYR 0.018 0.002 TYR I 390 ARG 0.004 0.000 ARG F 286 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 753) hydrogen bonds : angle 5.00616 ( 2089) covalent geometry : bond 0.00424 (29814) covalent geometry : angle 0.77740 (40742) Misc. bond : bond 0.00348 ( 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 359 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 276 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 PHE cc_start: 0.7440 (m-10) cc_final: 0.6953 (m-80) REVERT: A 320 LEU cc_start: 0.7215 (tp) cc_final: 0.6650 (pp) REVERT: A 346 MET cc_start: 0.7353 (tpp) cc_final: 0.5744 (tpp) REVERT: B 6 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8240 (t0) REVERT: B 138 ASN cc_start: 0.8446 (p0) cc_final: 0.7804 (t0) REVERT: C 252 ASP cc_start: 0.8197 (m-30) cc_final: 0.7889 (t0) REVERT: C 323 ASN cc_start: 0.6190 (OUTLIER) cc_final: 0.5438 (m-40) REVERT: C 347 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: D 71 HIS cc_start: 0.7807 (m-70) cc_final: 0.7491 (t-170) REVERT: E 252 ASP cc_start: 0.8590 (t0) cc_final: 0.8231 (t0) REVERT: F 188 SER cc_start: 0.8863 (m) cc_final: 0.8650 (p) REVERT: G 21 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.6906 (ptm160) REVERT: H 16 ASN cc_start: 0.8666 (t0) cc_final: 0.8409 (t0) REVERT: H 77 GLN cc_start: 0.7002 (mt0) cc_final: 0.6626 (tp-100) REVERT: H 88 ASN cc_start: 0.7390 (m-40) cc_final: 0.6748 (t0) REVERT: H 105 GLN cc_start: 0.8754 (tt0) cc_final: 0.8425 (tt0) REVERT: H 107 ILE cc_start: 0.8561 (mm) cc_final: 0.8318 (mt) REVERT: H 176 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.3709 (tm-30) REVERT: I 272 GLU cc_start: 0.8136 (pt0) cc_final: 0.7809 (mp0) REVERT: I 311 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8603 (tt) REVERT: I 333 ASN cc_start: 0.7813 (t0) cc_final: 0.7435 (p0) REVERT: J 43 ASP cc_start: 0.7993 (m-30) cc_final: 0.7758 (m-30) REVERT: J 308 GLU cc_start: 0.6259 (tm-30) cc_final: 0.5828 (tm-30) REVERT: J 323 MET cc_start: 0.4124 (tpp) cc_final: 0.3872 (tpp) REVERT: J 387 ARG cc_start: 0.6348 (tmt170) cc_final: 0.5992 (ptm-80) outliers start: 83 outliers final: 68 residues processed: 345 average time/residue: 0.3917 time to fit residues: 221.1265 Evaluate side-chains 339 residues out of total 3053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 265 time to evaluate : 3.188 ------------------------------------------------------------------------------- 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 B residue 6 ASN Chi-restraints excluded: chain B residue 17 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 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 191 VAL 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 213 LEU 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 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 123 ILE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 21 ARG 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 431 SER Chi-restraints excluded: chain G residue 524 THR Chi-restraints excluded: chain G residue 572 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 76 VAL 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 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 176 GLU Chi-restraints excluded: chain I residue 37 THR 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 198 CYS 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 151 HIS Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 106 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 315 optimal weight: 0.7980 chunk 39 optimal weight: 0.0020 chunk 223 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** 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 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 HIS ** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.149583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115607 restraints weight = 44502.638| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.95 r_work: 0.3075 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29816 Z= 0.141 Angle : 0.745 14.906 40742 Z= 0.381 Chirality : 0.045 0.300 4503 Planarity : 0.005 0.081 5002 Dihedral : 14.520 177.439 4661 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.44 % Allowed : 15.06 % Favored : 84.50 % Rotamer: Outliers : 2.66 % Allowed : 19.03 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.83 % Twisted Proline : 3.03 % Twisted General : 0.83 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.14), residues: 3400 helix: -0.64 (0.17), residues: 937 sheet: -0.55 (0.22), residues: 524 loop : -3.21 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 24 HIS 0.009 0.001 HIS G 272 PHE 0.018 0.001 PHE I 238 TYR 0.019 0.001 TYR I 390 ARG 0.003 0.000 ARG F 244 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 753) hydrogen bonds : angle 4.94783 ( 2089) covalent geometry : bond 0.00315 (29814) covalent geometry : angle 0.74474 (40742) Misc. bond : bond 0.00320 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14043.44 seconds wall clock time: 243 minutes 36.89 seconds (14616.89 seconds total)