Starting phenix.real_space_refine on Tue Jun 10 18:31:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rvn_19525/06_2025/8rvn_19525.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rvn_19525/06_2025/8rvn_19525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rvn_19525/06_2025/8rvn_19525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rvn_19525/06_2025/8rvn_19525.map" model { file = "/net/cci-nas-00/data/ceres_data/8rvn_19525/06_2025/8rvn_19525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rvn_19525/06_2025/8rvn_19525.cif" } resolution = 3.5 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= 0.004 sd= 0.115 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 7546 2.51 5 N 1937 2.21 5 O 2374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11924 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3370 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3377 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 424} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3377 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 424} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 864 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "L" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 768 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 7.75, per 1000 atoms: 0.65 Number of scatterers: 11924 At special positions: 0 Unit cell: (108.5, 99.82, 151.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 2374 8.00 N 1937 7.00 C 7546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS F 71 " - pdb=" SG CYS F 192 " distance=2.08 Simple disulfide: pdb=" SG CYS F 331 " - pdb=" SG CYS F 340 " distance=2.03 Simple disulfide: pdb=" SG CYS F 355 " - pdb=" SG CYS F 363 " distance=2.03 Simple disulfide: pdb=" SG CYS F 387 " - pdb=" SG CYS F 392 " distance=2.00 Simple disulfide: pdb=" SG CYS F 394 " - pdb=" SG CYS F 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 601 " - " ASN B 67 " " NAG B 602 " - " ASN B 99 " " NAG B 603 " - " ASN B 414 " " NAG B 604 " - " ASN B 464 " " NAG C 601 " - " ASN C 67 " " NAG C 602 " - " ASN C 99 " " NAG C 603 " - " ASN C 414 " " NAG C 604 " - " ASN C 464 " " NAG F 601 " - " ASN F 67 " " NAG F 602 " - " ASN F 99 " " NAG F 603 " - " ASN F 414 " " NAG F 604 " - " ASN F 464 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.7 seconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 23 sheets defined 33.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 65 through 69 removed outlier: 4.034A pdb=" N SER F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 101 Proline residue: F 89 - end of helix removed outlier: 3.624A pdb=" N ILE F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN F 100 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR F 101 " --> pdb=" O TYR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'F' and resid 125 through 137 Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 147 through 153 removed outlier: 3.705A pdb=" N SER F 153 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 182 Processing helix chain 'F' and resid 191 through 215 removed outlier: 3.967A pdb=" N PHE F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL F 213 " --> pdb=" O ASP F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 238 through 247 removed outlier: 3.904A pdb=" N LEU F 242 " --> pdb=" O ASN F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 349 through 357 Processing helix chain 'F' and resid 359 through 363 removed outlier: 3.523A pdb=" N LYS F 362 " --> pdb=" O SER F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 477 removed outlier: 4.474A pdb=" N SER F 457 " --> pdb=" O LYS F 453 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.715A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.758A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 100 removed outlier: 3.561A pdb=" N ASN B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Proline residue: B 89 - end of helix removed outlier: 3.795A pdb=" N ILE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.733A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.108A pdb=" N SER B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 191 through 211 Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.564A pdb=" N LEU B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 349 through 357 removed outlier: 4.187A pdb=" N CYS B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 removed outlier: 5.499A pdb=" N GLU B 361 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 477 removed outlier: 3.796A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.747A pdb=" N LYS C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 98 removed outlier: 3.582A pdb=" N GLY C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 3.927A pdb=" N ILE C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 124 through 146 removed outlier: 3.799A pdb=" N ALA C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.514A pdb=" N THR C 195 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.756A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.534A pdb=" N LYS C 362 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS C 363 " --> pdb=" O THR C 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 359 through 363' Processing helix chain 'C' and resid 452 through 477 removed outlier: 4.322A pdb=" N SER C 457 " --> pdb=" O LYS C 453 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'F' and resid 158 through 161 removed outlier: 5.248A pdb=" N TYR F 170 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL F 39 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU F 296 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY F 41 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLN F 294 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR F 43 " --> pdb=" O TYR F 292 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N TYR F 292 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N LYS F 45 " --> pdb=" O GLN F 290 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N GLN F 290 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS F 47 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE F 288 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS F 49 " --> pdb=" O THR F 286 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR F 286 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN F 51 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE F 284 " --> pdb=" O ASN F 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 275 through 297 current: chain 'F' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'F' and resid 226 through 227 removed outlier: 4.283A pdb=" N MET F 226 " --> pdb=" O GLY F 264 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR F 263 " --> pdb=" O TYR F 281 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE F 277 " --> pdb=" O ILE F 267 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL F 269 " --> pdb=" O TYR F 275 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR F 275 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE F 284 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN F 51 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR F 286 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS F 49 " --> pdb=" O THR F 286 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE F 288 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS F 47 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N GLN F 290 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N LYS F 45 " --> pdb=" O GLN F 290 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N TYR F 292 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR F 43 " --> pdb=" O TYR F 292 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLN F 294 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY F 41 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU F 296 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL F 39 " --> pdb=" O LEU F 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 39 through 60 current: chain 'F' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'F' and resid 114 through 116 removed outlier: 6.818A pdb=" N MET F 115 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'F' and resid 301 through 303 Processing sheet with id=AA6, first strand: chain 'F' and resid 376 through 379 Processing sheet with id=AA7, first strand: chain 'F' and resid 392 through 394 Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.516A pdb=" N VAL B 169 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 60 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL B 39 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU B 296 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY B 41 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLN B 294 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N THR B 43 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N TYR B 292 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N LYS B 45 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 10.468A pdb=" N GLN B 290 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS B 47 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 288 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 298 current: chain 'B' and resid 332 through 333 Processing sheet with id=AA9, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.245A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 288 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS B 47 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 10.468A pdb=" N GLN B 290 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N LYS B 45 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N TYR B 292 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N THR B 43 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLN B 294 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY B 41 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU B 296 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL B 39 " --> pdb=" O LEU B 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AB1, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AB3, first strand: chain 'B' and resid 308 through 310 Processing sheet with id=AB4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.550A pdb=" N CYS B 392 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 158 through 161 removed outlier: 5.257A pdb=" N TYR C 170 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU C 295 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR C 43 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 293 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS C 45 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ALA C 291 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N LYS C 47 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N GLN C 289 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N LYS C 49 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU C 287 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ASN C 51 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU C 285 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C 53 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS C 55 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR C 281 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE C 57 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ARG C 279 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE C 59 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE C 277 " --> pdb=" O ILE C 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 275 through 298 current: chain 'C' and resid 332 through 334 Processing sheet with id=AB6, first strand: chain 'C' and resid 226 through 227 removed outlier: 4.346A pdb=" N MET C 226 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR C 263 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE C 277 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE C 59 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ARG C 279 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE C 57 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TYR C 281 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS C 55 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C 53 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU C 285 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ASN C 51 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N GLU C 287 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N LYS C 49 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N GLN C 289 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N LYS C 47 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ALA C 291 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS C 45 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 293 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR C 43 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU C 295 " --> pdb=" O GLY C 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 60 current: chain 'C' and resid 322 through 326 removed outlier: 3.548A pdb=" N THR C 346 " --> pdb=" O ASN C 325 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AB9, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.016A pdb=" N GLU H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL H 76 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.535A pdb=" N GLN H 39 " --> pdb=" O THR H 89 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.535A pdb=" N GLN H 39 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AC4, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AC5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.466A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1986 1.31 - 1.44: 3000 1.44 - 1.57: 7017 1.57 - 1.69: 0 1.69 - 1.82: 99 Bond restraints: 12102 Sorted by residual: bond pdb=" C ASN F 464 " pdb=" O ASN F 464 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.63e+01 bond pdb=" C PRO C 298 " pdb=" O PRO C 298 " ideal model delta sigma weight residual 1.232 1.188 0.044 1.20e-02 6.94e+03 1.35e+01 bond pdb=" N ILE B 48 " pdb=" CA ILE B 48 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" C ARG C 353 " pdb=" O ARG C 353 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.16e-02 7.43e+03 1.06e+01 bond pdb=" N ILE F 190 " pdb=" CA ILE F 190 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.32e-02 5.74e+03 9.06e+00 ... (remaining 12097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 15915 1.98 - 3.97: 451 3.97 - 5.95: 63 5.95 - 7.93: 10 7.93 - 9.92: 4 Bond angle restraints: 16443 Sorted by residual: angle pdb=" N ILE C 96 " pdb=" CA ILE C 96 " pdb=" C ILE C 96 " ideal model delta sigma weight residual 111.58 104.69 6.89 1.06e+00 8.90e-01 4.22e+01 angle pdb=" C ASP C 413 " pdb=" N ASN C 414 " pdb=" CA ASN C 414 " ideal model delta sigma weight residual 120.28 128.44 -8.16 1.34e+00 5.57e-01 3.71e+01 angle pdb=" O LEU B 429 " pdb=" C LEU B 429 " pdb=" N GLY B 430 " ideal model delta sigma weight residual 123.10 117.12 5.98 1.15e+00 7.56e-01 2.71e+01 angle pdb=" C ASN F 99 " pdb=" CA ASN F 99 " pdb=" CB ASN F 99 " ideal model delta sigma weight residual 110.85 102.22 8.63 1.70e+00 3.46e-01 2.58e+01 angle pdb=" N ASN F 386 " pdb=" CA ASN F 386 " pdb=" C ASN F 386 " ideal model delta sigma weight residual 110.80 100.88 9.92 2.13e+00 2.20e-01 2.17e+01 ... (remaining 16438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6840 17.86 - 35.72: 556 35.72 - 53.58: 114 53.58 - 71.43: 22 71.43 - 89.29: 6 Dihedral angle restraints: 7538 sinusoidal: 3059 harmonic: 4479 Sorted by residual: dihedral pdb=" CB CYS F 387 " pdb=" SG CYS F 387 " pdb=" SG CYS F 392 " pdb=" CB CYS F 392 " ideal model delta sinusoidal sigma weight residual 93.00 154.21 -61.21 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CB CYS B 355 " pdb=" SG CYS B 355 " pdb=" SG CYS B 363 " pdb=" CB CYS B 363 " ideal model delta sinusoidal sigma weight residual 93.00 44.71 48.29 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS C 355 " pdb=" SG CYS C 355 " pdb=" SG CYS C 363 " pdb=" CB CYS C 363 " ideal model delta sinusoidal sigma weight residual -86.00 -130.44 44.44 1 1.00e+01 1.00e-02 2.75e+01 ... (remaining 7535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1760 0.075 - 0.151: 254 0.151 - 0.226: 15 0.226 - 0.302: 2 0.302 - 0.377: 1 Chirality restraints: 2032 Sorted by residual: chirality pdb=" C1 NAG B 603 " pdb=" ND2 ASN B 414 " pdb=" C2 NAG B 603 " pdb=" O5 NAG B 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C2 NAG C 603 " pdb=" C1 NAG C 603 " pdb=" C3 NAG C 603 " pdb=" N2 NAG C 603 " both_signs ideal model delta sigma weight residual False -2.49 -2.21 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 NAG C 601 " pdb=" C4 NAG C 601 " pdb=" C6 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.41 -2.64 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2029 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " 0.344 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG C 604 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " 0.121 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 601 " 0.329 2.00e-02 2.50e+03 2.77e-01 9.57e+02 pdb=" C7 NAG B 601 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG B 601 " 0.198 2.00e-02 2.50e+03 pdb=" N2 NAG B 601 " -0.476 2.00e-02 2.50e+03 pdb=" O7 NAG B 601 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 604 " -0.284 2.00e-02 2.50e+03 2.39e-01 7.17e+02 pdb=" C7 NAG B 604 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B 604 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG B 604 " 0.408 2.00e-02 2.50e+03 pdb=" O7 NAG B 604 " -0.016 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 53 2.54 - 3.13: 9395 3.13 - 3.72: 16788 3.72 - 4.31: 23565 4.31 - 4.90: 41037 Nonbonded interactions: 90838 Sorted by model distance: nonbonded pdb=" O ALA L 25 " pdb=" OG1 THR L 69 " model vdw 1.949 3.040 nonbonded pdb=" NZ LYS C 91 " pdb=" OE2 GLU C 95 " model vdw 2.142 3.120 nonbonded pdb=" OE1 GLU F 196 " pdb=" OH TYR L 32 " model vdw 2.142 3.040 nonbonded pdb=" OE2 GLU B 307 " pdb=" NH1 ARG B 375 " model vdw 2.170 3.120 nonbonded pdb=" OG1 THR B 334 " pdb=" O SER B 337 " model vdw 2.180 3.040 ... (remaining 90833 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 'B' and (resid 27 through 103 or resid 112 through 428 or resid 430 throu \ gh 477 or resid 601 through 604)) selection = (chain 'C' and (resid 27 through 103 or resid 112 through 428 or resid 430 throu \ gh 477 or resid 601 through 604)) selection = (chain 'F' and (resid 27 through 162 or resid 167 through 477 or resid 601 throu \ gh 604)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 30.100 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12131 Z= 0.257 Angle : 0.795 23.003 16513 Z= 0.464 Chirality : 0.050 0.377 2032 Planarity : 0.015 0.299 2058 Dihedral : 13.594 89.292 4605 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.30 % Allowed : 0.89 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1516 helix: 2.22 (0.28), residues: 399 sheet: -0.91 (0.27), residues: 351 loop : -1.38 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 62 HIS 0.004 0.001 HIS C 372 PHE 0.005 0.001 PHE L 62 TYR 0.015 0.001 TYR B 274 ARG 0.003 0.000 ARG B 336 Details of bonding type rmsd link_NAG-ASN : bond 0.01491 ( 12) link_NAG-ASN : angle 6.39840 ( 36) hydrogen bonds : bond 0.19239 ( 442) hydrogen bonds : angle 7.41962 ( 1290) SS BOND : bond 0.01471 ( 17) SS BOND : angle 3.23323 ( 34) covalent geometry : bond 0.00395 (12102) covalent geometry : angle 0.72403 (16443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 322 LEU cc_start: 0.8135 (mt) cc_final: 0.7777 (tp) REVERT: B 304 ASP cc_start: 0.7287 (t70) cc_final: 0.6946 (t70) REVERT: B 413 ASP cc_start: 0.8950 (p0) cc_final: 0.8571 (p0) REVERT: B 445 ILE cc_start: 0.7700 (tp) cc_final: 0.7493 (tp) REVERT: C 68 MET cc_start: 0.7539 (ptt) cc_final: 0.7082 (ptt) REVERT: C 244 ARG cc_start: 0.7387 (ttp80) cc_final: 0.7184 (mtp-110) REVERT: C 399 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7693 (mtm110) outliers start: 4 outliers final: 1 residues processed: 191 average time/residue: 0.2778 time to fit residues: 73.2227 Evaluate side-chains 147 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 387 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 119 optimal weight: 0.0050 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 138 optimal weight: 7.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.116562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.095980 restraints weight = 15709.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.098882 restraints weight = 10523.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.100955 restraints weight = 7915.014| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12131 Z= 0.138 Angle : 0.641 10.764 16513 Z= 0.313 Chirality : 0.047 0.305 2032 Planarity : 0.004 0.036 2058 Dihedral : 5.892 56.902 1886 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.12 % Allowed : 7.16 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1516 helix: 2.06 (0.27), residues: 423 sheet: -0.73 (0.27), residues: 341 loop : -1.23 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 62 HIS 0.002 0.001 HIS C 372 PHE 0.013 0.001 PHE L 62 TYR 0.015 0.001 TYR B 248 ARG 0.006 0.001 ARG C 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 12) link_NAG-ASN : angle 3.44993 ( 36) hydrogen bonds : bond 0.04285 ( 442) hydrogen bonds : angle 5.26242 ( 1290) SS BOND : bond 0.00424 ( 17) SS BOND : angle 1.34018 ( 34) covalent geometry : bond 0.00317 (12102) covalent geometry : angle 0.61892 (16443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 322 LEU cc_start: 0.8119 (mt) cc_final: 0.7670 (tp) REVERT: B 304 ASP cc_start: 0.7263 (t70) cc_final: 0.6883 (t70) REVERT: C 375 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.8086 (mtt90) REVERT: C 399 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7659 (mtm110) outliers start: 15 outliers final: 12 residues processed: 159 average time/residue: 0.2738 time to fit residues: 60.6980 Evaluate side-chains 158 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 387 CYS Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 139 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN B 176 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 37 GLN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.117014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.096343 restraints weight = 15895.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.099347 restraints weight = 10551.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.101378 restraints weight = 7829.490| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12131 Z= 0.111 Angle : 0.560 9.015 16513 Z= 0.277 Chirality : 0.045 0.349 2032 Planarity : 0.003 0.035 2058 Dihedral : 5.420 58.010 1886 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.42 % Allowed : 10.14 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1516 helix: 2.06 (0.27), residues: 429 sheet: -0.56 (0.27), residues: 339 loop : -1.27 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS C 372 PHE 0.009 0.001 PHE B 376 TYR 0.013 0.001 TYR B 248 ARG 0.003 0.000 ARG F 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 12) link_NAG-ASN : angle 3.05027 ( 36) hydrogen bonds : bond 0.03607 ( 442) hydrogen bonds : angle 4.81122 ( 1290) SS BOND : bond 0.00458 ( 17) SS BOND : angle 1.13549 ( 34) covalent geometry : bond 0.00249 (12102) covalent geometry : angle 0.54062 (16443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6154 (m) cc_final: 0.5269 (m) REVERT: F 322 LEU cc_start: 0.8083 (mt) cc_final: 0.7588 (tp) REVERT: F 392 CYS cc_start: 0.5913 (p) cc_final: 0.5709 (p) REVERT: B 287 GLU cc_start: 0.6862 (tt0) cc_final: 0.6659 (tt0) REVERT: B 304 ASP cc_start: 0.7124 (t70) cc_final: 0.6615 (t70) REVERT: B 336 ARG cc_start: 0.8017 (tpp-160) cc_final: 0.7816 (tpp-160) REVERT: C 375 ARG cc_start: 0.8242 (mtt-85) cc_final: 0.8026 (mtt90) REVERT: C 399 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7664 (mtm110) outliers start: 19 outliers final: 15 residues processed: 162 average time/residue: 0.2759 time to fit residues: 61.8973 Evaluate side-chains 158 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.115486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.093890 restraints weight = 15837.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.097137 restraints weight = 10276.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.099367 restraints weight = 7532.999| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12131 Z= 0.152 Angle : 0.577 9.037 16513 Z= 0.288 Chirality : 0.046 0.342 2032 Planarity : 0.003 0.036 2058 Dihedral : 5.374 58.669 1885 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.94 % Allowed : 11.63 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1516 helix: 2.06 (0.27), residues: 428 sheet: -0.57 (0.27), residues: 344 loop : -1.29 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 308 HIS 0.003 0.001 HIS C 372 PHE 0.010 0.001 PHE L 62 TYR 0.020 0.001 TYR B 473 ARG 0.003 0.000 ARG F 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 12) link_NAG-ASN : angle 2.86537 ( 36) hydrogen bonds : bond 0.03865 ( 442) hydrogen bonds : angle 4.73066 ( 1290) SS BOND : bond 0.00396 ( 17) SS BOND : angle 1.06424 ( 34) covalent geometry : bond 0.00370 (12102) covalent geometry : angle 0.56062 (16443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 322 LEU cc_start: 0.8172 (mt) cc_final: 0.7617 (tp) REVERT: F 392 CYS cc_start: 0.5815 (p) cc_final: 0.5534 (p) REVERT: B 287 GLU cc_start: 0.6963 (tt0) cc_final: 0.6737 (tt0) REVERT: B 304 ASP cc_start: 0.7334 (t70) cc_final: 0.6723 (t70) REVERT: C 399 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7657 (mtm110) outliers start: 26 outliers final: 17 residues processed: 161 average time/residue: 0.2709 time to fit residues: 61.2523 Evaluate side-chains 157 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 131 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.0370 chunk 121 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.113989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.093132 restraints weight = 15908.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.096093 restraints weight = 10678.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.098183 restraints weight = 8002.331| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12131 Z= 0.170 Angle : 0.588 9.898 16513 Z= 0.296 Chirality : 0.047 0.334 2032 Planarity : 0.003 0.036 2058 Dihedral : 5.459 58.195 1885 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.86 % Allowed : 13.20 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1516 helix: 2.01 (0.27), residues: 428 sheet: -0.61 (0.26), residues: 344 loop : -1.35 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 308 HIS 0.003 0.001 HIS C 372 PHE 0.011 0.001 PHE F 282 TYR 0.020 0.001 TYR B 473 ARG 0.004 0.000 ARG F 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 12) link_NAG-ASN : angle 2.71514 ( 36) hydrogen bonds : bond 0.04055 ( 442) hydrogen bonds : angle 4.71467 ( 1290) SS BOND : bond 0.00416 ( 17) SS BOND : angle 1.08907 ( 34) covalent geometry : bond 0.00417 (12102) covalent geometry : angle 0.57302 (16443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6473 (m) cc_final: 0.5810 (m) REVERT: F 322 LEU cc_start: 0.8259 (mt) cc_final: 0.7684 (tp) REVERT: F 372 HIS cc_start: 0.7269 (m170) cc_final: 0.7027 (m170) REVERT: F 392 CYS cc_start: 0.5813 (p) cc_final: 0.5509 (p) REVERT: B 258 GLU cc_start: 0.8149 (tp30) cc_final: 0.7867 (tp30) REVERT: B 287 GLU cc_start: 0.7053 (tt0) cc_final: 0.6847 (tt0) REVERT: B 304 ASP cc_start: 0.7384 (t70) cc_final: 0.6856 (t70) REVERT: C 399 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7640 (mtm110) outliers start: 25 outliers final: 22 residues processed: 165 average time/residue: 0.2650 time to fit residues: 62.5185 Evaluate side-chains 165 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 254 ASP Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 352 MET Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 47 optimal weight: 0.3980 chunk 63 optimal weight: 0.4980 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.117550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.096110 restraints weight = 15922.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.099429 restraints weight = 10152.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.101783 restraints weight = 7358.500| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12131 Z= 0.103 Angle : 0.527 10.396 16513 Z= 0.267 Chirality : 0.045 0.321 2032 Planarity : 0.003 0.038 2058 Dihedral : 5.382 58.883 1885 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.57 % Allowed : 13.94 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1516 helix: 2.13 (0.27), residues: 429 sheet: -0.51 (0.26), residues: 346 loop : -1.31 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 308 HIS 0.004 0.001 HIS C 372 PHE 0.007 0.001 PHE B 376 TYR 0.020 0.001 TYR B 473 ARG 0.004 0.000 ARG F 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00381 ( 12) link_NAG-ASN : angle 2.39934 ( 36) hydrogen bonds : bond 0.03226 ( 442) hydrogen bonds : angle 4.48702 ( 1290) SS BOND : bond 0.00278 ( 17) SS BOND : angle 0.91501 ( 34) covalent geometry : bond 0.00227 (12102) covalent geometry : angle 0.51475 (16443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6385 (m) cc_final: 0.5703 (m) REVERT: B 258 GLU cc_start: 0.8202 (tp30) cc_final: 0.7889 (tp30) REVERT: B 304 ASP cc_start: 0.7379 (t70) cc_final: 0.6828 (t70) REVERT: C 399 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7604 (mtm110) REVERT: C 437 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7853 (p0) outliers start: 21 outliers final: 16 residues processed: 156 average time/residue: 0.2608 time to fit residues: 58.1636 Evaluate side-chains 158 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.0570 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.114694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.093886 restraints weight = 15914.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.096908 restraints weight = 10592.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.099006 restraints weight = 7876.489| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12131 Z= 0.153 Angle : 0.563 11.515 16513 Z= 0.285 Chirality : 0.046 0.315 2032 Planarity : 0.003 0.037 2058 Dihedral : 5.484 57.950 1885 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.86 % Allowed : 14.32 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1516 helix: 2.06 (0.27), residues: 428 sheet: -0.55 (0.26), residues: 346 loop : -1.33 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 308 HIS 0.004 0.001 HIS C 372 PHE 0.010 0.001 PHE F 282 TYR 0.019 0.001 TYR B 473 ARG 0.004 0.000 ARG L 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 12) link_NAG-ASN : angle 2.41920 ( 36) hydrogen bonds : bond 0.03745 ( 442) hydrogen bonds : angle 4.55374 ( 1290) SS BOND : bond 0.00397 ( 17) SS BOND : angle 0.98486 ( 34) covalent geometry : bond 0.00373 (12102) covalent geometry : angle 0.55116 (16443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6568 (m) cc_final: 0.5912 (m) REVERT: F 322 LEU cc_start: 0.8118 (mt) cc_final: 0.7622 (tp) REVERT: F 392 CYS cc_start: 0.5895 (p) cc_final: 0.5536 (p) REVERT: B 258 GLU cc_start: 0.8212 (tp30) cc_final: 0.7884 (tp30) REVERT: B 304 ASP cc_start: 0.7438 (t70) cc_final: 0.6879 (t70) REVERT: C 399 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7625 (mtm110) REVERT: C 437 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7879 (p0) REVERT: L 74 THR cc_start: 0.8741 (m) cc_final: 0.8365 (p) outliers start: 25 outliers final: 20 residues processed: 160 average time/residue: 0.2523 time to fit residues: 57.7881 Evaluate side-chains 162 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 18 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN B 29 HIS ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.115725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.094335 restraints weight = 16032.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.097582 restraints weight = 10233.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.099804 restraints weight = 7456.860| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12131 Z= 0.125 Angle : 0.535 9.069 16513 Z= 0.274 Chirality : 0.045 0.310 2032 Planarity : 0.003 0.037 2058 Dihedral : 5.531 58.391 1885 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.16 % Allowed : 14.02 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1516 helix: 2.07 (0.27), residues: 429 sheet: -0.49 (0.26), residues: 346 loop : -1.33 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 308 HIS 0.006 0.001 HIS B 29 PHE 0.008 0.001 PHE B 376 TYR 0.018 0.001 TYR B 473 ARG 0.003 0.000 ARG L 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 12) link_NAG-ASN : angle 2.29544 ( 36) hydrogen bonds : bond 0.03473 ( 442) hydrogen bonds : angle 4.47744 ( 1290) SS BOND : bond 0.00327 ( 17) SS BOND : angle 0.92086 ( 34) covalent geometry : bond 0.00295 (12102) covalent geometry : angle 0.52407 (16443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6550 (m) cc_final: 0.5871 (m) REVERT: F 322 LEU cc_start: 0.8065 (mt) cc_final: 0.7553 (tp) REVERT: F 392 CYS cc_start: 0.5927 (p) cc_final: 0.5578 (p) REVERT: B 258 GLU cc_start: 0.8196 (tp30) cc_final: 0.7728 (tp30) REVERT: B 304 ASP cc_start: 0.7464 (t70) cc_final: 0.6909 (t70) REVERT: C 399 ARG cc_start: 0.7922 (mtm-85) cc_final: 0.7631 (mtm110) REVERT: C 437 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7883 (p0) REVERT: L 74 THR cc_start: 0.8718 (m) cc_final: 0.8355 (p) outliers start: 29 outliers final: 23 residues processed: 163 average time/residue: 0.2526 time to fit residues: 59.1104 Evaluate side-chains 165 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 23 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 150 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 119 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.115983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.094560 restraints weight = 15895.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.097804 restraints weight = 10142.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.100131 restraints weight = 7393.103| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12131 Z= 0.124 Angle : 0.539 10.976 16513 Z= 0.275 Chirality : 0.045 0.304 2032 Planarity : 0.003 0.037 2058 Dihedral : 5.564 58.175 1885 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.01 % Allowed : 14.69 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1516 helix: 2.07 (0.27), residues: 429 sheet: -0.45 (0.26), residues: 346 loop : -1.35 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 308 HIS 0.004 0.001 HIS C 372 PHE 0.009 0.001 PHE B 376 TYR 0.018 0.001 TYR B 473 ARG 0.004 0.000 ARG L 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 12) link_NAG-ASN : angle 2.24031 ( 36) hydrogen bonds : bond 0.03416 ( 442) hydrogen bonds : angle 4.44517 ( 1290) SS BOND : bond 0.00322 ( 17) SS BOND : angle 0.89817 ( 34) covalent geometry : bond 0.00291 (12102) covalent geometry : angle 0.52781 (16443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6490 (m) cc_final: 0.5801 (m) REVERT: F 322 LEU cc_start: 0.8055 (mt) cc_final: 0.7527 (tp) REVERT: F 392 CYS cc_start: 0.5945 (p) cc_final: 0.5586 (p) REVERT: B 258 GLU cc_start: 0.8233 (tp30) cc_final: 0.7750 (tp30) REVERT: B 304 ASP cc_start: 0.7516 (t70) cc_final: 0.6967 (t70) REVERT: C 399 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7630 (mtm110) REVERT: C 437 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7890 (p0) REVERT: L 19 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7554 (p) REVERT: L 74 THR cc_start: 0.8714 (m) cc_final: 0.8371 (p) outliers start: 27 outliers final: 23 residues processed: 164 average time/residue: 0.2512 time to fit residues: 59.2769 Evaluate side-chains 167 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 103 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 133 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.116850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.095535 restraints weight = 15701.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.098768 restraints weight = 10080.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.101040 restraints weight = 7364.981| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12131 Z= 0.118 Angle : 0.537 12.516 16513 Z= 0.274 Chirality : 0.045 0.299 2032 Planarity : 0.003 0.038 2058 Dihedral : 5.567 59.371 1885 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.01 % Allowed : 15.21 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1516 helix: 2.09 (0.27), residues: 429 sheet: -0.40 (0.27), residues: 344 loop : -1.35 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 308 HIS 0.004 0.001 HIS C 372 PHE 0.009 0.001 PHE B 376 TYR 0.017 0.001 TYR B 473 ARG 0.004 0.000 ARG L 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 12) link_NAG-ASN : angle 2.15592 ( 36) hydrogen bonds : bond 0.03301 ( 442) hydrogen bonds : angle 4.39932 ( 1290) SS BOND : bond 0.00302 ( 17) SS BOND : angle 0.85419 ( 34) covalent geometry : bond 0.00274 (12102) covalent geometry : angle 0.52670 (16443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6540 (m) cc_final: 0.5871 (m) REVERT: F 322 LEU cc_start: 0.8050 (mt) cc_final: 0.7522 (tp) REVERT: F 392 CYS cc_start: 0.5865 (p) cc_final: 0.5496 (p) REVERT: B 258 GLU cc_start: 0.8220 (tp30) cc_final: 0.7899 (tp30) REVERT: B 304 ASP cc_start: 0.7538 (t70) cc_final: 0.6999 (t70) REVERT: C 399 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7636 (mtm110) REVERT: C 437 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7897 (p0) REVERT: L 19 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7557 (p) REVERT: L 74 THR cc_start: 0.8708 (m) cc_final: 0.8391 (p) outliers start: 27 outliers final: 24 residues processed: 163 average time/residue: 0.2440 time to fit residues: 57.0763 Evaluate side-chains 169 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 302 ASN Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 352 MET Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 341 ASN Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 82 optimal weight: 0.1980 chunk 95 optimal weight: 0.4980 chunk 143 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.116606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.095154 restraints weight = 15809.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.098412 restraints weight = 10143.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.100733 restraints weight = 7402.744| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12131 Z= 0.117 Angle : 0.535 12.678 16513 Z= 0.273 Chirality : 0.045 0.296 2032 Planarity : 0.003 0.041 2058 Dihedral : 5.566 59.878 1885 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.01 % Allowed : 15.36 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1516 helix: 2.17 (0.27), residues: 423 sheet: -0.36 (0.27), residues: 344 loop : -1.32 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 308 HIS 0.004 0.001 HIS C 372 PHE 0.008 0.001 PHE B 376 TYR 0.017 0.001 TYR B 473 ARG 0.010 0.000 ARG C 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 12) link_NAG-ASN : angle 2.10178 ( 36) hydrogen bonds : bond 0.03277 ( 442) hydrogen bonds : angle 4.37429 ( 1290) SS BOND : bond 0.00312 ( 17) SS BOND : angle 0.85886 ( 34) covalent geometry : bond 0.00272 (12102) covalent geometry : angle 0.52591 (16443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3770.84 seconds wall clock time: 66 minutes 30.82 seconds (3990.82 seconds total)