Starting phenix.real_space_refine on Wed Sep 17 22:39:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rvn_19525/09_2025/8rvn_19525.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rvn_19525/09_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_19525/09_2025/8rvn_19525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rvn_19525/09_2025/8rvn_19525.map" model { file = "/net/cci-nas-00/data/ceres_data/8rvn_19525/09_2025/8rvn_19525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rvn_19525/09_2025/8rvn_19525.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.33, per 1000 atoms: 0.28 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: 1.00 Conformation dependent library (CDL) restraints added in 624.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.51 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: 2.08 Time building geometry restraints manager: 1.38 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 604)) selection = (chain 'C' and (resid 27 through 103 or resid 112 through 428 or resid 430 throu \ gh 604)) selection = (chain 'F' and (resid 27 through 162 or resid 167 through 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: 1.640 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.370 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (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 ARG 0.003 0.000 ARG B 336 TYR 0.015 0.001 TYR B 274 PHE 0.005 0.001 PHE L 62 TRP 0.007 0.001 TRP H 62 HIS 0.004 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00395 (12102) covalent geometry : angle 0.72403 (16443) SS BOND : bond 0.01471 ( 17) SS BOND : angle 3.23323 ( 34) hydrogen bonds : bond 0.19239 ( 442) hydrogen bonds : angle 7.41962 ( 1290) link_NAG-ASN : bond 0.01491 ( 12) link_NAG-ASN : angle 6.39840 ( 36) *********************** 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 : 0.538 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: 0.1412 time to fit residues: 37.1117 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 : 0.477 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** 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 = 0.115535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.094789 restraints weight = 15849.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.097730 restraints weight = 10611.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.099804 restraints weight = 7943.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.101325 restraints weight = 6399.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.102357 restraints weight = 5409.822| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12131 Z= 0.155 Angle : 0.651 10.873 16513 Z= 0.318 Chirality : 0.048 0.322 2032 Planarity : 0.004 0.036 2058 Dihedral : 5.910 55.904 1886 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.42 % Allowed : 7.61 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.22), residues: 1516 helix: 2.00 (0.27), residues: 423 sheet: -0.77 (0.27), residues: 341 loop : -1.26 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 353 TYR 0.015 0.001 TYR B 248 PHE 0.014 0.001 PHE L 62 TRP 0.007 0.001 TRP C 308 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00364 (12102) covalent geometry : angle 0.62998 (16443) SS BOND : bond 0.00659 ( 17) SS BOND : angle 1.38022 ( 34) hydrogen bonds : bond 0.04413 ( 442) hydrogen bonds : angle 5.23384 ( 1290) link_NAG-ASN : bond 0.00524 ( 12) link_NAG-ASN : angle 3.37269 ( 36) *********************** 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 172 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 70 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8449 (mt0) REVERT: F 322 LEU cc_start: 0.8135 (mt) cc_final: 0.7681 (tp) REVERT: B 304 ASP cc_start: 0.7259 (t70) cc_final: 0.6878 (t70) REVERT: C 244 ARG cc_start: 0.7462 (ttp80) cc_final: 0.7261 (mtp-110) REVERT: C 375 ARG cc_start: 0.8291 (mtt-85) cc_final: 0.8071 (mtt90) REVERT: C 399 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7644 (mtm110) outliers start: 19 outliers final: 14 residues processed: 164 average time/residue: 0.1376 time to fit residues: 31.3687 Evaluate side-chains 161 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 23 CYS 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 34 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 70 optimal weight: 0.0670 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 6 GLN L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.115974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.095220 restraints weight = 16003.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.098142 restraints weight = 10651.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.100213 restraints weight = 7949.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.101707 restraints weight = 6377.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.102870 restraints weight = 5388.281| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12131 Z= 0.123 Angle : 0.575 8.980 16513 Z= 0.285 Chirality : 0.046 0.352 2032 Planarity : 0.003 0.035 2058 Dihedral : 5.493 57.899 1886 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.34 % Allowed : 10.51 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.22), residues: 1516 helix: 2.06 (0.27), residues: 424 sheet: -0.63 (0.27), residues: 339 loop : -1.29 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 336 TYR 0.013 0.001 TYR B 248 PHE 0.009 0.001 PHE B 376 TRP 0.007 0.001 TRP C 308 HIS 0.003 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00285 (12102) covalent geometry : angle 0.55540 (16443) SS BOND : bond 0.00375 ( 17) SS BOND : angle 1.11759 ( 34) hydrogen bonds : bond 0.03822 ( 442) hydrogen bonds : angle 4.86310 ( 1290) link_NAG-ASN : bond 0.00495 ( 12) link_NAG-ASN : angle 3.12550 ( 36) *********************** 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 169 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6503 (m) cc_final: 0.5729 (m) REVERT: F 322 LEU cc_start: 0.8140 (mt) cc_final: 0.7632 (tp) REVERT: F 392 CYS cc_start: 0.5943 (p) cc_final: 0.5734 (p) REVERT: B 304 ASP cc_start: 0.7121 (t70) cc_final: 0.6612 (t70) REVERT: C 375 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.8043 (mtt90) REVERT: C 399 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7649 (mtm110) outliers start: 18 outliers final: 14 residues processed: 160 average time/residue: 0.1392 time to fit residues: 30.7666 Evaluate side-chains 157 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 70 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 105 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.115376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.093628 restraints weight = 16034.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.096913 restraints weight = 10382.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.099214 restraints weight = 7588.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.100667 restraints weight = 6017.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.101947 restraints weight = 5091.369| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12131 Z= 0.148 Angle : 0.575 9.034 16513 Z= 0.287 Chirality : 0.046 0.345 2032 Planarity : 0.003 0.037 2058 Dihedral : 5.411 58.717 1885 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.72 % Allowed : 11.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.22), residues: 1516 helix: 2.01 (0.27), residues: 428 sheet: -0.62 (0.27), residues: 341 loop : -1.31 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 336 TYR 0.014 0.001 TYR L 49 PHE 0.010 0.001 PHE F 282 TRP 0.008 0.001 TRP C 308 HIS 0.003 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00357 (12102) covalent geometry : angle 0.55821 (16443) SS BOND : bond 0.00408 ( 17) SS BOND : angle 1.14713 ( 34) hydrogen bonds : bond 0.03881 ( 442) hydrogen bonds : angle 4.74669 ( 1290) link_NAG-ASN : bond 0.00440 ( 12) link_NAG-ASN : angle 2.88415 ( 36) *********************** 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 168 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6387 (m) cc_final: 0.5694 (m) REVERT: F 322 LEU cc_start: 0.8194 (mt) cc_final: 0.7659 (tp) REVERT: F 392 CYS cc_start: 0.5878 (p) cc_final: 0.5586 (p) REVERT: B 304 ASP cc_start: 0.7286 (t70) cc_final: 0.6692 (t70) REVERT: C 399 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7632 (mtm110) outliers start: 23 outliers final: 15 residues processed: 157 average time/residue: 0.1351 time to fit residues: 29.7251 Evaluate side-chains 153 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 378 LEU 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 95 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.115724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.094089 restraints weight = 15818.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.097287 restraints weight = 10243.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.099582 restraints weight = 7532.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.101142 restraints weight = 5983.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.102360 restraints weight = 5034.885| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1719 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= 0.136 Angle : 0.566 10.028 16513 Z= 0.284 Chirality : 0.046 0.335 2032 Planarity : 0.003 0.037 2058 Dihedral : 5.395 58.513 1885 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.79 % Allowed : 12.68 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.22), residues: 1516 helix: 2.03 (0.27), residues: 428 sheet: -0.59 (0.27), residues: 342 loop : -1.33 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 375 TYR 0.013 0.001 TYR L 49 PHE 0.009 0.001 PHE B 376 TRP 0.008 0.001 TRP C 308 HIS 0.003 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00324 (12102) covalent geometry : angle 0.55168 (16443) SS BOND : bond 0.00345 ( 17) SS BOND : angle 0.96871 ( 34) hydrogen bonds : bond 0.03691 ( 442) hydrogen bonds : angle 4.65920 ( 1290) link_NAG-ASN : bond 0.00416 ( 12) link_NAG-ASN : angle 2.68977 ( 36) *********************** 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 171 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6471 (m) cc_final: 0.5785 (m) REVERT: F 322 LEU cc_start: 0.8209 (mt) cc_final: 0.7688 (tp) REVERT: F 392 CYS cc_start: 0.5839 (p) cc_final: 0.5539 (p) REVERT: B 304 ASP cc_start: 0.7294 (t70) cc_final: 0.6719 (t70) REVERT: C 399 ARG cc_start: 0.7884 (mtm-85) cc_final: 0.7613 (mtm110) outliers start: 24 outliers final: 21 residues processed: 161 average time/residue: 0.1367 time to fit residues: 30.8866 Evaluate side-chains 160 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 C residue 76 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 99 optimal weight: 0.0070 chunk 146 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.115508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.093928 restraints weight = 15892.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.097153 restraints weight = 10270.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.099436 restraints weight = 7541.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.101005 restraints weight = 5980.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.102276 restraints weight = 5021.111| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12131 Z= 0.136 Angle : 0.557 10.798 16513 Z= 0.280 Chirality : 0.046 0.326 2032 Planarity : 0.003 0.038 2058 Dihedral : 5.417 58.414 1885 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.94 % Allowed : 13.65 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.22), residues: 1516 helix: 2.06 (0.27), residues: 428 sheet: -0.58 (0.26), residues: 346 loop : -1.32 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 336 TYR 0.013 0.001 TYR L 49 PHE 0.009 0.001 PHE B 376 TRP 0.008 0.001 TRP C 308 HIS 0.003 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00326 (12102) covalent geometry : angle 0.54286 (16443) SS BOND : bond 0.00395 ( 17) SS BOND : angle 1.03735 ( 34) hydrogen bonds : bond 0.03653 ( 442) hydrogen bonds : angle 4.59166 ( 1290) link_NAG-ASN : bond 0.00382 ( 12) link_NAG-ASN : angle 2.56077 ( 36) *********************** 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 166 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6459 (m) cc_final: 0.5799 (m) REVERT: F 322 LEU cc_start: 0.8197 (mt) cc_final: 0.7641 (tp) REVERT: B 304 ASP cc_start: 0.7311 (t70) cc_final: 0.6797 (t70) REVERT: C 399 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7605 (mtm110) REVERT: C 437 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7847 (p0) outliers start: 26 outliers final: 21 residues processed: 157 average time/residue: 0.1251 time to fit residues: 28.1360 Evaluate side-chains 159 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 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 463 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 Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.0040 chunk 115 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.116918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.095561 restraints weight = 15808.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.098732 restraints weight = 10132.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.101065 restraints weight = 7428.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.102600 restraints weight = 5871.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.103836 restraints weight = 4932.676| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12131 Z= 0.112 Angle : 0.530 11.476 16513 Z= 0.268 Chirality : 0.045 0.315 2032 Planarity : 0.003 0.038 2058 Dihedral : 5.429 58.501 1885 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.24 % Allowed : 13.80 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.22), residues: 1516 helix: 2.12 (0.27), residues: 429 sheet: -0.50 (0.26), residues: 346 loop : -1.29 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 336 TYR 0.011 0.001 TYR F 135 PHE 0.008 0.001 PHE B 376 TRP 0.008 0.001 TRP C 308 HIS 0.004 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00256 (12102) covalent geometry : angle 0.51838 (16443) SS BOND : bond 0.00299 ( 17) SS BOND : angle 0.87783 ( 34) hydrogen bonds : bond 0.03319 ( 442) hydrogen bonds : angle 4.48520 ( 1290) link_NAG-ASN : bond 0.00351 ( 12) link_NAG-ASN : angle 2.35555 ( 36) *********************** 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 172 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6474 (m) cc_final: 0.5823 (m) REVERT: F 322 LEU cc_start: 0.8219 (mt) cc_final: 0.7640 (tp) REVERT: F 392 CYS cc_start: 0.5977 (p) cc_final: 0.5637 (p) REVERT: B 304 ASP cc_start: 0.7318 (t70) cc_final: 0.6799 (t70) REVERT: C 399 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7587 (mtm110) REVERT: C 437 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7852 (p0) REVERT: L 74 THR cc_start: 0.8728 (m) cc_final: 0.8349 (p) outliers start: 30 outliers final: 23 residues processed: 162 average time/residue: 0.1195 time to fit residues: 27.9746 Evaluate side-chains 163 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 352 MET Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 463 MET 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 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 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 70 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 149 optimal weight: 0.0170 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.0570 chunk 97 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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** L 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.095721 restraints weight = 15812.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.099039 restraints weight = 10156.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.101373 restraints weight = 7385.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.103001 restraints weight = 5829.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.104128 restraints weight = 4886.599| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12131 Z= 0.107 Angle : 0.523 12.100 16513 Z= 0.266 Chirality : 0.045 0.307 2032 Planarity : 0.003 0.038 2058 Dihedral : 5.454 58.394 1885 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.94 % Allowed : 14.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.22), residues: 1516 helix: 2.15 (0.27), residues: 429 sheet: -0.43 (0.27), residues: 344 loop : -1.30 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 336 TYR 0.010 0.001 TYR L 49 PHE 0.008 0.001 PHE B 376 TRP 0.007 0.001 TRP C 308 HIS 0.005 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00243 (12102) covalent geometry : angle 0.51235 (16443) SS BOND : bond 0.00290 ( 17) SS BOND : angle 0.86479 ( 34) hydrogen bonds : bond 0.03158 ( 442) hydrogen bonds : angle 4.39139 ( 1290) link_NAG-ASN : bond 0.00325 ( 12) link_NAG-ASN : angle 2.21806 ( 36) *********************** 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 167 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6494 (m) cc_final: 0.5834 (m) REVERT: F 392 CYS cc_start: 0.6038 (p) cc_final: 0.5696 (p) REVERT: B 304 ASP cc_start: 0.7327 (t70) cc_final: 0.6801 (t70) REVERT: C 399 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7605 (mtm110) REVERT: C 437 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7887 (p0) REVERT: L 74 THR cc_start: 0.8724 (m) cc_final: 0.8378 (p) outliers start: 26 outliers final: 22 residues processed: 158 average time/residue: 0.1224 time to fit residues: 27.7687 Evaluate side-chains 162 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 352 MET Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 463 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 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 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 102 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.116643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.094991 restraints weight = 15766.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.098237 restraints weight = 10162.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.100565 restraints weight = 7424.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.102219 restraints weight = 5874.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.103378 restraints weight = 4903.723| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12131 Z= 0.122 Angle : 0.535 12.804 16513 Z= 0.272 Chirality : 0.045 0.301 2032 Planarity : 0.003 0.037 2058 Dihedral : 5.507 58.655 1885 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.24 % Allowed : 14.54 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.22), residues: 1516 helix: 2.13 (0.27), residues: 429 sheet: -0.42 (0.27), residues: 344 loop : -1.31 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 399 TYR 0.012 0.001 TYR L 49 PHE 0.009 0.001 PHE B 376 TRP 0.008 0.001 TRP C 308 HIS 0.004 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00286 (12102) covalent geometry : angle 0.52454 (16443) SS BOND : bond 0.00333 ( 17) SS BOND : angle 0.86351 ( 34) hydrogen bonds : bond 0.03309 ( 442) hydrogen bonds : angle 4.39605 ( 1290) link_NAG-ASN : bond 0.00328 ( 12) link_NAG-ASN : angle 2.19790 ( 36) *********************** 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 174 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6489 (m) cc_final: 0.5829 (m) REVERT: F 322 LEU cc_start: 0.8090 (mp) cc_final: 0.7419 (tp) REVERT: F 392 CYS cc_start: 0.6062 (p) cc_final: 0.5714 (p) REVERT: B 304 ASP cc_start: 0.7396 (t70) cc_final: 0.6844 (t70) REVERT: C 399 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7610 (mtm110) REVERT: C 437 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7829 (p0) REVERT: L 19 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7577 (p) REVERT: L 74 THR cc_start: 0.8723 (m) cc_final: 0.8388 (p) outliers start: 30 outliers final: 25 residues processed: 163 average time/residue: 0.1202 time to fit residues: 28.3473 Evaluate side-chains 166 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 F residue 463 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 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 380 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 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 87 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.115738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.094799 restraints weight = 15942.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.097790 restraints weight = 10578.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.099892 restraints weight = 7878.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.101465 restraints weight = 6322.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.102586 restraints weight = 5342.127| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12131 Z= 0.133 Angle : 0.544 12.982 16513 Z= 0.277 Chirality : 0.045 0.301 2032 Planarity : 0.003 0.037 2058 Dihedral : 5.561 58.757 1885 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.01 % Allowed : 14.99 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.22), residues: 1516 helix: 2.10 (0.27), residues: 429 sheet: -0.44 (0.27), residues: 344 loop : -1.31 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 399 TYR 0.012 0.001 TYR L 49 PHE 0.009 0.001 PHE B 376 TRP 0.008 0.001 TRP C 308 HIS 0.004 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00319 (12102) covalent geometry : angle 0.53424 (16443) SS BOND : bond 0.00355 ( 17) SS BOND : angle 0.93522 ( 34) hydrogen bonds : bond 0.03429 ( 442) hydrogen bonds : angle 4.41444 ( 1290) link_NAG-ASN : bond 0.00330 ( 12) link_NAG-ASN : angle 2.18304 ( 36) ********************** 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 170 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 71 CYS cc_start: 0.6391 (m) cc_final: 0.5637 (m) REVERT: F 322 LEU cc_start: 0.8099 (mp) cc_final: 0.7398 (tp) REVERT: B 304 ASP cc_start: 0.7450 (t70) cc_final: 0.6901 (t70) REVERT: C 399 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7609 (mtm110) REVERT: C 437 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7837 (p0) REVERT: L 19 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7708 (p) REVERT: L 74 THR cc_start: 0.8722 (m) cc_final: 0.8397 (p) outliers start: 27 outliers final: 24 residues processed: 160 average time/residue: 0.1248 time to fit residues: 28.8750 Evaluate side-chains 167 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP 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 F residue 463 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 422 LEU 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 30 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN C 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.112791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.091838 restraints weight = 15987.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.094698 restraints weight = 10693.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.096865 restraints weight = 8009.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.098310 restraints weight = 6444.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.099452 restraints weight = 5473.039| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12131 Z= 0.188 Angle : 0.600 13.282 16513 Z= 0.305 Chirality : 0.047 0.312 2032 Planarity : 0.004 0.037 2058 Dihedral : 5.752 58.043 1885 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.09 % Allowed : 15.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.22), residues: 1516 helix: 1.98 (0.27), residues: 428 sheet: -0.56 (0.27), residues: 344 loop : -1.38 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 399 TYR 0.016 0.001 TYR L 49 PHE 0.012 0.001 PHE B 376 TRP 0.009 0.002 TRP C 308 HIS 0.004 0.001 HIS C 372 Details of bonding type rmsd covalent geometry : bond 0.00465 (12102) covalent geometry : angle 0.58780 (16443) SS BOND : bond 0.00493 ( 17) SS BOND : angle 1.18975 ( 34) hydrogen bonds : bond 0.04256 ( 442) hydrogen bonds : angle 4.65190 ( 1290) link_NAG-ASN : bond 0.00456 ( 12) link_NAG-ASN : angle 2.39956 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2070.99 seconds wall clock time: 36 minutes 46.91 seconds (2206.91 seconds total)