Starting phenix.real_space_refine on Tue Jul 29 23:18:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dg8_27418/07_2025/8dg8_27418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg8_27418/07_2025/8dg8_27418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dg8_27418/07_2025/8dg8_27418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg8_27418/07_2025/8dg8_27418.map" model { file = "/net/cci-nas-00/data/ceres_data/8dg8_27418/07_2025/8dg8_27418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg8_27418/07_2025/8dg8_27418.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.167 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 60 5.16 5 C 7323 2.51 5 N 1943 2.21 5 O 2291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11617 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3251 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 955 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Chain: "A" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3251 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3251 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 406} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.25, per 1000 atoms: 0.71 Number of scatterers: 11617 At special positions: 0 Unit cell: (124.491, 104.943, 117.289, 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 60 16.00 O 2291 8.00 N 1943 7.00 C 7323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 230 " 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 H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 230 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 230 " 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 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 A 601 " - " ASN A 238 " " NAG A 602 " - " ASN A 359 " " NAG A 603 " - " ASN A 446 " " NAG B 601 " - " ASN B 238 " " NAG B 602 " - " ASN B 359 " " NAG B 603 " - " ASN B 446 " " NAG C 601 " - " ASN C 238 " " NAG C 602 " - " ASN C 359 " " NAG C 603 " - " ASN C 446 " Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.7 seconds 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2794 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 24 sheets defined 29.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.500A pdb=" N LYS B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 124 through 152 removed outlier: 4.090A pdb=" N ALA B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.699A pdb=" N LYS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 184 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 4.559A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 210 removed outlier: 3.594A pdb=" N LEU B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.927A pdb=" N TYR B 235 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.866A pdb=" N ILE B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.637A pdb=" N LEU B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 452 through 471 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 100A through 100E removed outlier: 4.376A pdb=" N TRP H 100D" --> pdb=" O ASP H 100A" (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.760A pdb=" N GLN A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 74' Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.590A pdb=" N ILE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 124 through 152 removed outlier: 3.542A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 195 through 215 removed outlier: 4.613A pdb=" N CYS A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 245 through 250 removed outlier: 4.450A pdb=" N LYS A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 349 through 356 removed outlier: 4.034A pdb=" N LEU A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 469 removed outlier: 3.612A pdb=" N LYS A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 71 removed outlier: 4.267A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.521A pdb=" N ASP C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.978A pdb=" N ALA C 133 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.595A pdb=" N ALA C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 190 removed outlier: 4.134A pdb=" N VAL C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 4.993A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 214 removed outlier: 3.517A pdb=" N ASN C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.625A pdb=" N ILE C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 removed outlier: 4.213A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE C 258 " --> pdb=" O TYR C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 358 removed outlier: 4.011A pdb=" N LEU C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 469 removed outlier: 3.869A pdb=" N LEU C 467 " --> pdb=" O VAL C 463 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 469 " --> pdb=" O SER C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 472 No H-bonds generated for 'chain 'C' and resid 470 through 472' Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.080A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 281 through 286 removed outlier: 4.528A pdb=" N ASN B 43 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N THR B 286 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N SER B 41 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.721A pdb=" N ASP B 268 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 226 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AA5, first strand: chain 'B' and resid 376 through 377 removed outlier: 3.534A pdb=" N ALA B 385 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.146A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.146A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.723A pdb=" N THR L 105 " --> pdb=" O VAL L 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 50 removed outlier: 6.899A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.501A pdb=" N ASP A 297 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.501A pdb=" N ASP A 297 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN A 43 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 286 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER A 41 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A 288 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS A 39 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N ASN A 290 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLY A 37 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 158 through 164 removed outlier: 3.621A pdb=" N SER A 163 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASN A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 48 " --> pdb=" O CYS A 168 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 170 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 172 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 268 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN A 279 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL A 266 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 226 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AB7, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.695A pdb=" N ALA A 385 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AB9, first strand: chain 'C' and resid 285 through 286 removed outlier: 4.973A pdb=" N LYS C 295 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 293 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLY C 37 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR C 291 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 285 through 286 removed outlier: 8.047A pdb=" N TYR C 338 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY C 37 " --> pdb=" O TYR C 338 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N CYS C 340 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS C 39 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 158 through 161 removed outlier: 3.629A pdb=" N VAL C 161 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 169 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N VAL C 170 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR C 48 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE C 172 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 50 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 268 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AC4, first strand: chain 'C' and resid 301 through 303 removed outlier: 4.350A pdb=" N THR C 367 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 376 through 377 Processing sheet with id=AC6, first strand: chain 'C' and resid 392 through 394 387 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.95 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3800 1.34 - 1.46: 2514 1.46 - 1.59: 5398 1.59 - 1.71: 0 1.71 - 1.84: 74 Bond restraints: 11786 Sorted by residual: bond pdb=" CA SER B 357 " pdb=" CB SER B 357 " ideal model delta sigma weight residual 1.528 1.469 0.059 1.34e-02 5.57e+03 1.96e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" CA SER B 361 " pdb=" CB SER B 361 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.69e-02 3.50e+03 1.05e+01 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" N SER B 361 " pdb=" CA SER B 361 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.82e+00 ... (remaining 11781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15627 2.07 - 4.14: 298 4.14 - 6.22: 51 6.22 - 8.29: 10 8.29 - 10.36: 2 Bond angle restraints: 15988 Sorted by residual: angle pdb=" CA ASN B 359 " pdb=" CB ASN B 359 " pdb=" CG ASN B 359 " ideal model delta sigma weight residual 112.60 105.66 6.94 1.00e+00 1.00e+00 4.82e+01 angle pdb=" N SER B 357 " pdb=" CA SER B 357 " pdb=" C SER B 357 " ideal model delta sigma weight residual 111.87 103.19 8.68 1.41e+00 5.03e-01 3.79e+01 angle pdb=" N VAL B 328 " pdb=" CA VAL B 328 " pdb=" C VAL B 328 " ideal model delta sigma weight residual 111.91 107.52 4.39 8.90e-01 1.26e+00 2.44e+01 angle pdb=" C ASN A 380 " pdb=" CA ASN A 380 " pdb=" CB ASN A 380 " ideal model delta sigma weight residual 116.63 110.91 5.72 1.16e+00 7.43e-01 2.44e+01 angle pdb=" C LEU B 356 " pdb=" N SER B 357 " pdb=" CA SER B 357 " ideal model delta sigma weight residual 122.79 116.34 6.45 1.63e+00 3.76e-01 1.57e+01 ... (remaining 15983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.02: 6994 25.02 - 50.04: 312 50.04 - 75.06: 34 75.06 - 100.08: 14 100.08 - 125.10: 1 Dihedral angle restraints: 7355 sinusoidal: 3024 harmonic: 4331 Sorted by residual: dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -9.36 -76.64 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A 213 " pdb=" SG CYS A 213 " pdb=" SG CYS A 230 " pdb=" CB CYS A 230 " ideal model delta sinusoidal sigma weight residual -86.00 -162.25 76.25 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS B 162 " pdb=" SG CYS B 162 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 38.72 54.28 1 1.00e+01 1.00e-02 4.00e+01 ... (remaining 7352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1733 0.077 - 0.153: 201 0.153 - 0.230: 6 0.230 - 0.306: 2 0.306 - 0.383: 3 Chirality restraints: 1945 Sorted by residual: chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 359 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE A 50 " pdb=" CA ILE A 50 " pdb=" CG1 ILE A 50 " pdb=" CG2 ILE A 50 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CB ILE B 50 " pdb=" CA ILE B 50 " pdb=" CG1 ILE B 50 " pdb=" CG2 ILE B 50 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 1942 not shown) Planarity restraints: 2035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.279 2.00e-02 2.50e+03 2.37e-01 7.03e+02 pdb=" C7 NAG B 602 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.409 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 356 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C LEU B 356 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU B 356 " -0.029 2.00e-02 2.50e+03 pdb=" N SER B 357 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 238 " -0.001 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN A 238 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 238 " -0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN A 238 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.036 2.00e-02 2.50e+03 ... (remaining 2032 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 358 2.68 - 3.24: 12316 3.24 - 3.79: 17549 3.79 - 4.35: 23828 4.35 - 4.90: 37648 Nonbonded interactions: 91699 Sorted by model distance: nonbonded pdb=" OH TYR C 251 " pdb=" O PRO C 283 " model vdw 2.129 3.040 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLY C 396 " model vdw 2.145 3.040 nonbonded pdb=" ND2 ASN A 349 " pdb=" OD1 ASP C 455 " model vdw 2.154 3.120 nonbonded pdb=" NE2 GLN C 403 " pdb=" O GLY C 408 " model vdw 2.195 3.120 nonbonded pdb=" O ILE C 151 " pdb=" NZ LYS C 173 " model vdw 2.198 3.120 ... (remaining 91694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.160 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 31.400 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 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 0.087 11818 Z= 0.181 Angle : 0.757 21.870 16061 Z= 0.399 Chirality : 0.049 0.383 1945 Planarity : 0.007 0.237 2026 Dihedral : 14.018 125.103 4492 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.37 % Favored : 91.56 % Rotamer: Outliers : 0.15 % Allowed : 0.31 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.20), residues: 1470 helix: -1.54 (0.26), residues: 379 sheet: -1.41 (0.31), residues: 273 loop : -2.25 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 HIS 0.005 0.001 HIS C 414 PHE 0.009 0.001 PHE L 62 TYR 0.014 0.001 TYR A 83 ARG 0.004 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.01139 ( 9) link_NAG-ASN : angle 5.95840 ( 27) hydrogen bonds : bond 0.29256 ( 373) hydrogen bonds : angle 10.13912 ( 1038) SS BOND : bond 0.00375 ( 23) SS BOND : angle 0.88145 ( 46) covalent geometry : bond 0.00363 (11786) covalent geometry : angle 0.71670 (15988) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 208 SER cc_start: 0.6852 (m) cc_final: 0.6531 (p) REVERT: B 281 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6930 (ptt180) REVERT: B 284 LEU cc_start: 0.6724 (tp) cc_final: 0.6132 (mt) REVERT: B 289 LEU cc_start: 0.7135 (mt) cc_final: 0.6892 (mp) REVERT: B 425 MET cc_start: 0.4509 (mtp) cc_final: 0.4245 (mtm) REVERT: H 3 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6608 (pm20) REVERT: H 89 VAL cc_start: 0.8152 (m) cc_final: 0.7674 (p) REVERT: H 100 GLU cc_start: 0.6064 (tp30) cc_final: 0.5388 (tt0) REVERT: L 31 TYR cc_start: 0.6902 (m-80) cc_final: 0.6577 (m-80) REVERT: L 32 TYR cc_start: 0.6470 (m-10) cc_final: 0.5910 (m-10) REVERT: A 70 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8214 (mm-40) REVERT: A 78 LEU cc_start: 0.6034 (pp) cc_final: 0.5593 (tt) REVERT: A 270 ASP cc_start: 0.5827 (t0) cc_final: 0.5350 (t0) REVERT: A 414 HIS cc_start: 0.4695 (p-80) cc_final: 0.4436 (p-80) REVERT: A 462 LYS cc_start: 0.7438 (ttpp) cc_final: 0.7016 (tmmt) REVERT: C 48 TYR cc_start: 0.7629 (m-80) cc_final: 0.6894 (m-80) REVERT: C 49 LEU cc_start: 0.5722 (mt) cc_final: 0.5363 (mp) REVERT: C 56 LYS cc_start: 0.7100 (tmtt) cc_final: 0.6883 (tppp) REVERT: C 236 ARG cc_start: 0.7090 (mtt90) cc_final: 0.5386 (mmt180) REVERT: C 278 LEU cc_start: 0.7413 (mp) cc_final: 0.7103 (mt) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.2243 time to fit residues: 68.3198 Evaluate side-chains 152 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 38 optimal weight: 0.0470 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.0020 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 ASN B 461 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN A 155 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 206 HIS C 290 ASN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.243422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.235368 restraints weight = 10483.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.218761 restraints weight = 13935.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.218586 restraints weight = 13665.013| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11818 Z= 0.149 Angle : 0.744 9.067 16061 Z= 0.380 Chirality : 0.051 0.322 1945 Planarity : 0.005 0.095 2026 Dihedral : 8.660 115.516 1780 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 1.38 % Allowed : 8.20 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 1470 helix: -1.32 (0.25), residues: 377 sheet: -1.40 (0.31), residues: 276 loop : -2.19 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 308 HIS 0.007 0.001 HIS C 414 PHE 0.020 0.002 PHE A 437 TYR 0.024 0.002 TYR C 71 ARG 0.005 0.001 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 9) link_NAG-ASN : angle 2.70150 ( 27) hydrogen bonds : bond 0.05364 ( 373) hydrogen bonds : angle 6.75488 ( 1038) SS BOND : bond 0.00389 ( 23) SS BOND : angle 0.99192 ( 46) covalent geometry : bond 0.00325 (11786) covalent geometry : angle 0.73546 (15988) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 VAL cc_start: 0.8568 (m) cc_final: 0.8361 (m) REVERT: B 284 LEU cc_start: 0.7484 (tp) cc_final: 0.7250 (mt) REVERT: B 289 LEU cc_start: 0.7560 (mt) cc_final: 0.7336 (mp) REVERT: A 78 LEU cc_start: 0.5771 (pp) cc_final: 0.5457 (tt) REVERT: A 209 GLU cc_start: 0.7111 (tp30) cc_final: 0.5935 (mt-10) REVERT: A 437 PHE cc_start: 0.7373 (t80) cc_final: 0.6969 (t80) REVERT: C 48 TYR cc_start: 0.8151 (m-80) cc_final: 0.7498 (m-80) REVERT: C 158 VAL cc_start: 0.7229 (t) cc_final: 0.6890 (p) REVERT: C 236 ARG cc_start: 0.6793 (mtt90) cc_final: 0.5565 (mmt180) outliers start: 18 outliers final: 8 residues processed: 174 average time/residue: 0.2321 time to fit residues: 58.5006 Evaluate side-chains 126 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain C residue 370 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 111 optimal weight: 0.0570 chunk 14 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 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 = 0.4691 r_free = 0.4691 target = 0.244913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.236705 restraints weight = 10760.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.219047 restraints weight = 15567.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.220238 restraints weight = 15180.094| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11818 Z= 0.140 Angle : 0.695 10.366 16061 Z= 0.355 Chirality : 0.049 0.365 1945 Planarity : 0.004 0.070 2026 Dihedral : 7.997 107.610 1777 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.28 % Favored : 92.65 % Rotamer: Outliers : 2.61 % Allowed : 11.26 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.21), residues: 1470 helix: -1.12 (0.26), residues: 375 sheet: -1.26 (0.29), residues: 288 loop : -2.12 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 308 HIS 0.010 0.001 HIS A 414 PHE 0.019 0.002 PHE A 437 TYR 0.022 0.002 TYR L 32 ARG 0.003 0.000 ARG C 73 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 9) link_NAG-ASN : angle 2.26836 ( 27) hydrogen bonds : bond 0.04225 ( 373) hydrogen bonds : angle 6.13005 ( 1038) SS BOND : bond 0.00353 ( 23) SS BOND : angle 1.04859 ( 46) covalent geometry : bond 0.00315 (11786) covalent geometry : angle 0.68802 (15988) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5273 (OUTLIER) cc_final: 0.5058 (tp) REVERT: B 289 LEU cc_start: 0.7727 (mt) cc_final: 0.7482 (mp) REVERT: H 68 THR cc_start: 0.5592 (t) cc_final: 0.5353 (p) REVERT: A 417 CYS cc_start: 0.6159 (t) cc_final: 0.5434 (t) REVERT: A 437 PHE cc_start: 0.7398 (t80) cc_final: 0.7139 (t80) REVERT: C 158 VAL cc_start: 0.7291 (t) cc_final: 0.6950 (p) REVERT: C 231 ILE cc_start: 0.6076 (mm) cc_final: 0.5645 (mt) REVERT: C 236 ARG cc_start: 0.6798 (mtt90) cc_final: 0.5546 (mmt180) outliers start: 34 outliers final: 15 residues processed: 162 average time/residue: 0.3238 time to fit residues: 74.7033 Evaluate side-chains 130 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 135 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 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 = 0.4677 r_free = 0.4677 target = 0.242718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.234181 restraints weight = 10558.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.220281 restraints weight = 14387.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.218135 restraints weight = 15110.125| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11818 Z= 0.157 Angle : 0.688 10.578 16061 Z= 0.353 Chirality : 0.049 0.351 1945 Planarity : 0.004 0.057 2026 Dihedral : 7.566 97.966 1777 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.23 % Favored : 91.70 % Rotamer: Outliers : 3.60 % Allowed : 12.87 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.21), residues: 1470 helix: -1.01 (0.27), residues: 379 sheet: -1.21 (0.30), residues: 288 loop : -2.21 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 308 HIS 0.013 0.002 HIS A 414 PHE 0.034 0.002 PHE A 378 TYR 0.023 0.002 TYR L 32 ARG 0.003 0.000 ARG C 73 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 9) link_NAG-ASN : angle 2.20885 ( 27) hydrogen bonds : bond 0.03728 ( 373) hydrogen bonds : angle 5.78628 ( 1038) SS BOND : bond 0.00328 ( 23) SS BOND : angle 0.95591 ( 46) covalent geometry : bond 0.00370 (11786) covalent geometry : angle 0.68169 (15988) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5459 (OUTLIER) cc_final: 0.5150 (tp) REVERT: A 417 CYS cc_start: 0.6227 (t) cc_final: 0.5607 (t) REVERT: C 38 MET cc_start: 0.6846 (tpt) cc_final: 0.6407 (tpt) REVERT: C 153 ASP cc_start: 0.7429 (p0) cc_final: 0.7228 (p0) REVERT: C 158 VAL cc_start: 0.7270 (t) cc_final: 0.6974 (p) REVERT: C 231 ILE cc_start: 0.5943 (mm) cc_final: 0.5604 (mt) REVERT: C 236 ARG cc_start: 0.6733 (mtt90) cc_final: 0.5507 (mmt180) outliers start: 47 outliers final: 26 residues processed: 166 average time/residue: 0.3390 time to fit residues: 81.2590 Evaluate side-chains 152 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 82 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 61 optimal weight: 0.0070 chunk 68 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 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 = 0.4420 r_free = 0.4420 target = 0.220353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.212627 restraints weight = 10956.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.210727 restraints weight = 15132.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.210213 restraints weight = 17597.970| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11818 Z= 0.137 Angle : 0.668 10.897 16061 Z= 0.339 Chirality : 0.048 0.334 1945 Planarity : 0.004 0.052 2026 Dihedral : 7.135 91.103 1777 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.62 % Favored : 92.31 % Rotamer: Outliers : 3.45 % Allowed : 14.71 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.21), residues: 1470 helix: -0.86 (0.27), residues: 381 sheet: -1.26 (0.31), residues: 286 loop : -2.12 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 308 HIS 0.013 0.001 HIS A 414 PHE 0.020 0.002 PHE A 378 TYR 0.015 0.002 TYR L 49 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 9) link_NAG-ASN : angle 2.10559 ( 27) hydrogen bonds : bond 0.03416 ( 373) hydrogen bonds : angle 5.50294 ( 1038) SS BOND : bond 0.00287 ( 23) SS BOND : angle 0.77417 ( 46) covalent geometry : bond 0.00319 (11786) covalent geometry : angle 0.66248 (15988) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5686 (OUTLIER) cc_final: 0.5333 (tp) REVERT: A 417 CYS cc_start: 0.6150 (t) cc_final: 0.5574 (t) REVERT: A 434 THR cc_start: 0.7861 (t) cc_final: 0.7553 (m) REVERT: C 53 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7657 (mt) REVERT: C 153 ASP cc_start: 0.6428 (p0) cc_final: 0.6169 (p0) REVERT: C 158 VAL cc_start: 0.7209 (t) cc_final: 0.6964 (p) REVERT: C 231 ILE cc_start: 0.5795 (mm) cc_final: 0.5506 (mt) REVERT: C 236 ARG cc_start: 0.6169 (mtt90) cc_final: 0.5340 (mmt180) outliers start: 45 outliers final: 27 residues processed: 163 average time/residue: 0.4824 time to fit residues: 116.8531 Evaluate side-chains 155 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 120 optimal weight: 4.9990 chunk 75 optimal weight: 0.0470 chunk 43 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 90 optimal weight: 0.0970 chunk 105 optimal weight: 0.0670 chunk 91 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN B 380 ASN B 395 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.222235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.214523 restraints weight = 11045.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.213785 restraints weight = 16091.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.213554 restraints weight = 15853.975| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11818 Z= 0.125 Angle : 0.666 12.378 16061 Z= 0.336 Chirality : 0.047 0.296 1945 Planarity : 0.004 0.052 2026 Dihedral : 6.837 85.887 1777 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 3.75 % Allowed : 15.79 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.21), residues: 1470 helix: -0.70 (0.27), residues: 379 sheet: -1.16 (0.31), residues: 281 loop : -2.07 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 308 HIS 0.013 0.001 HIS A 414 PHE 0.019 0.001 PHE A 437 TYR 0.013 0.001 TYR L 49 ARG 0.013 0.000 ARG A 73 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 9) link_NAG-ASN : angle 2.04675 ( 27) hydrogen bonds : bond 0.03221 ( 373) hydrogen bonds : angle 5.22616 ( 1038) SS BOND : bond 0.00263 ( 23) SS BOND : angle 1.19764 ( 46) covalent geometry : bond 0.00274 (11786) covalent geometry : angle 0.65957 (15988) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5668 (OUTLIER) cc_final: 0.5339 (tp) REVERT: B 172 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7865 (mt) REVERT: A 417 CYS cc_start: 0.6098 (t) cc_final: 0.5576 (t) REVERT: A 434 THR cc_start: 0.7963 (t) cc_final: 0.7628 (m) REVERT: A 460 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6269 (pp) REVERT: C 31 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7315 (tp) REVERT: C 53 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7602 (mt) REVERT: C 153 ASP cc_start: 0.6469 (p0) cc_final: 0.6200 (p0) REVERT: C 158 VAL cc_start: 0.7144 (t) cc_final: 0.6893 (p) REVERT: C 231 ILE cc_start: 0.5736 (mm) cc_final: 0.5456 (mt) REVERT: C 236 ARG cc_start: 0.6025 (mtt90) cc_final: 0.5253 (mmt180) outliers start: 49 outliers final: 27 residues processed: 159 average time/residue: 0.2205 time to fit residues: 51.5285 Evaluate side-chains 150 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 413 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 127 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.219701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.212592 restraints weight = 11160.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.200990 restraints weight = 16595.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.197321 restraints weight = 17736.431| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11818 Z= 0.145 Angle : 0.685 11.166 16061 Z= 0.346 Chirality : 0.048 0.278 1945 Planarity : 0.004 0.054 2026 Dihedral : 6.771 81.437 1777 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.11 % Rotamer: Outliers : 3.07 % Allowed : 16.93 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.21), residues: 1470 helix: -0.76 (0.27), residues: 378 sheet: -1.11 (0.31), residues: 289 loop : -2.12 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 308 HIS 0.012 0.001 HIS A 414 PHE 0.020 0.002 PHE A 437 TYR 0.015 0.002 TYR A 309 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 9) link_NAG-ASN : angle 2.11349 ( 27) hydrogen bonds : bond 0.03382 ( 373) hydrogen bonds : angle 5.25468 ( 1038) SS BOND : bond 0.00277 ( 23) SS BOND : angle 1.27389 ( 46) covalent geometry : bond 0.00340 (11786) covalent geometry : angle 0.67733 (15988) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 2.306 Fit side-chains revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5546 (OUTLIER) cc_final: 0.5252 (tp) REVERT: B 312 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6715 (mt) REVERT: H 82 MET cc_start: 0.7489 (tpp) cc_final: 0.7111 (tpp) REVERT: A 417 CYS cc_start: 0.6218 (t) cc_final: 0.5745 (t) REVERT: A 434 THR cc_start: 0.7871 (t) cc_final: 0.7551 (m) REVERT: A 437 PHE cc_start: 0.7412 (t80) cc_final: 0.6986 (t80) REVERT: A 460 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6381 (pp) REVERT: C 31 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7113 (tp) REVERT: C 53 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7741 (mt) REVERT: C 153 ASP cc_start: 0.7028 (p0) cc_final: 0.6722 (p0) REVERT: C 158 VAL cc_start: 0.7314 (t) cc_final: 0.7011 (p) REVERT: C 231 ILE cc_start: 0.5990 (mm) cc_final: 0.5535 (mt) REVERT: C 236 ARG cc_start: 0.6451 (mtt90) cc_final: 0.5345 (mmt180) outliers start: 40 outliers final: 30 residues processed: 153 average time/residue: 0.3025 time to fit residues: 69.5943 Evaluate side-chains 152 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 135 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 33 optimal weight: 0.0470 chunk 7 optimal weight: 0.3980 chunk 75 optimal weight: 0.0270 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 14 optimal weight: 0.0060 overall best weight: 0.1752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 ASN H 3 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.215574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.204901 restraints weight = 11274.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.201615 restraints weight = 16765.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.201079 restraints weight = 18171.193| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11818 Z= 0.119 Angle : 0.663 11.081 16061 Z= 0.333 Chirality : 0.047 0.270 1945 Planarity : 0.004 0.054 2026 Dihedral : 6.520 75.707 1777 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.01 % Favored : 92.86 % Rotamer: Outliers : 2.53 % Allowed : 17.78 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.21), residues: 1470 helix: -0.67 (0.28), residues: 378 sheet: -0.97 (0.31), residues: 285 loop : -2.06 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 308 HIS 0.011 0.002 HIS A 414 PHE 0.021 0.002 PHE A 44 TYR 0.012 0.001 TYR L 49 ARG 0.007 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 9) link_NAG-ASN : angle 2.04628 ( 27) hydrogen bonds : bond 0.03132 ( 373) hydrogen bonds : angle 5.12274 ( 1038) SS BOND : bond 0.00283 ( 23) SS BOND : angle 0.92257 ( 46) covalent geometry : bond 0.00254 (11786) covalent geometry : angle 0.65734 (15988) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.497 Fit side-chains revert: symmetry clash REVERT: B 288 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7159 (mt) REVERT: A 417 CYS cc_start: 0.6178 (t) cc_final: 0.5705 (t) REVERT: A 434 THR cc_start: 0.7678 (t) cc_final: 0.7456 (m) REVERT: A 437 PHE cc_start: 0.7386 (t80) cc_final: 0.6866 (t80) REVERT: C 31 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7091 (tp) REVERT: C 38 MET cc_start: 0.6515 (tpt) cc_final: 0.6028 (tpt) REVERT: C 53 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7607 (mt) REVERT: C 153 ASP cc_start: 0.6805 (p0) cc_final: 0.6511 (p0) REVERT: C 158 VAL cc_start: 0.7242 (t) cc_final: 0.6955 (p) REVERT: C 231 ILE cc_start: 0.5732 (mm) cc_final: 0.5216 (mt) REVERT: C 236 ARG cc_start: 0.6409 (mtt90) cc_final: 0.5335 (mmt180) REVERT: C 422 ILE cc_start: 0.6071 (OUTLIER) cc_final: 0.5846 (pp) outliers start: 33 outliers final: 22 residues processed: 147 average time/residue: 0.3018 time to fit residues: 65.4420 Evaluate side-chains 145 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 422 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 140 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95BHIS C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.217708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.210878 restraints weight = 11249.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.207312 restraints weight = 15187.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.206221 restraints weight = 23655.809| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11818 Z= 0.163 Angle : 0.706 11.138 16061 Z= 0.356 Chirality : 0.049 0.256 1945 Planarity : 0.004 0.054 2026 Dihedral : 6.599 72.694 1777 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.23 % Favored : 91.63 % Rotamer: Outliers : 2.84 % Allowed : 17.62 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.21), residues: 1470 helix: -0.77 (0.27), residues: 380 sheet: -1.08 (0.31), residues: 285 loop : -2.11 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 308 HIS 0.014 0.002 HIS A 414 PHE 0.019 0.002 PHE A 378 TYR 0.021 0.002 TYR A 309 ARG 0.004 0.000 ARG A 73 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 9) link_NAG-ASN : angle 2.20292 ( 27) hydrogen bonds : bond 0.03334 ( 373) hydrogen bonds : angle 5.22604 ( 1038) SS BOND : bond 0.00314 ( 23) SS BOND : angle 0.93328 ( 46) covalent geometry : bond 0.00392 (11786) covalent geometry : angle 0.70048 (15988) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5721 (OUTLIER) cc_final: 0.5419 (tp) REVERT: B 288 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7308 (mt) REVERT: A 317 MET cc_start: 0.7743 (ttp) cc_final: 0.7525 (ttm) REVERT: A 417 CYS cc_start: 0.6222 (t) cc_final: 0.5817 (t) REVERT: A 434 THR cc_start: 0.7761 (t) cc_final: 0.7507 (m) REVERT: A 437 PHE cc_start: 0.7371 (t80) cc_final: 0.6933 (t80) REVERT: A 460 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6584 (pp) REVERT: C 31 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7214 (tp) REVERT: C 38 MET cc_start: 0.6487 (tpt) cc_final: 0.5961 (tpt) REVERT: C 53 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7615 (mt) REVERT: C 153 ASP cc_start: 0.6723 (p0) cc_final: 0.6420 (p0) REVERT: C 158 VAL cc_start: 0.7359 (t) cc_final: 0.7064 (p) REVERT: C 231 ILE cc_start: 0.5761 (mm) cc_final: 0.5337 (mt) REVERT: C 236 ARG cc_start: 0.6271 (mtt90) cc_final: 0.5325 (mmt180) REVERT: C 422 ILE cc_start: 0.6217 (OUTLIER) cc_final: 0.5981 (pp) outliers start: 37 outliers final: 30 residues processed: 146 average time/residue: 0.3934 time to fit residues: 85.9910 Evaluate side-chains 148 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.218663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.211407 restraints weight = 11097.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.197557 restraints weight = 15930.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.195125 restraints weight = 21187.160| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11818 Z= 0.149 Angle : 0.692 11.761 16061 Z= 0.347 Chirality : 0.048 0.254 1945 Planarity : 0.004 0.055 2026 Dihedral : 6.562 70.236 1777 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.30 % Favored : 91.56 % Rotamer: Outliers : 2.99 % Allowed : 17.93 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.21), residues: 1470 helix: -0.76 (0.27), residues: 374 sheet: -1.03 (0.31), residues: 280 loop : -2.13 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 308 HIS 0.014 0.002 HIS A 414 PHE 0.022 0.002 PHE A 243 TYR 0.015 0.002 TYR A 309 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 9) link_NAG-ASN : angle 2.19933 ( 27) hydrogen bonds : bond 0.03249 ( 373) hydrogen bonds : angle 5.17294 ( 1038) SS BOND : bond 0.00270 ( 23) SS BOND : angle 0.87869 ( 46) covalent geometry : bond 0.00355 (11786) covalent geometry : angle 0.68631 (15988) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2940 Ramachandran restraints generated. 1470 Oldfield, 0 Emsley, 1470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 ILE cc_start: 0.5514 (OUTLIER) cc_final: 0.5233 (tp) REVERT: B 395 ASN cc_start: 0.6209 (OUTLIER) cc_final: 0.5988 (t0) REVERT: A 317 MET cc_start: 0.7769 (ttp) cc_final: 0.7527 (ttm) REVERT: A 460 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6615 (pp) REVERT: C 31 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7215 (tp) REVERT: C 38 MET cc_start: 0.6537 (tpt) cc_final: 0.5992 (tpt) REVERT: C 53 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7714 (mt) REVERT: C 153 ASP cc_start: 0.7155 (p0) cc_final: 0.6803 (p0) REVERT: C 158 VAL cc_start: 0.7433 (t) cc_final: 0.7112 (p) REVERT: C 231 ILE cc_start: 0.5925 (mm) cc_final: 0.5481 (mt) REVERT: C 236 ARG cc_start: 0.6510 (mtt90) cc_final: 0.5394 (mmt180) REVERT: C 422 ILE cc_start: 0.6225 (OUTLIER) cc_final: 0.5964 (pp) outliers start: 39 outliers final: 30 residues processed: 144 average time/residue: 0.3335 time to fit residues: 70.6596 Evaluate side-chains 146 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 125 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 72 optimal weight: 0.0170 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 395 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 155 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 = 0.4409 r_free = 0.4409 target = 0.218547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.211447 restraints weight = 11053.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.198041 restraints weight = 16054.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.193356 restraints weight = 16370.712| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11818 Z= 0.148 Angle : 0.696 12.049 16061 Z= 0.349 Chirality : 0.048 0.252 1945 Planarity : 0.004 0.056 2026 Dihedral : 6.503 67.406 1777 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.44 % Favored : 91.43 % Rotamer: Outliers : 2.99 % Allowed : 18.47 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.21), residues: 1470 helix: -0.76 (0.27), residues: 380 sheet: -0.98 (0.31), residues: 280 loop : -2.12 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 308 HIS 0.014 0.002 HIS A 414 PHE 0.020 0.002 PHE A 243 TYR 0.015 0.002 TYR A 309 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 9) link_NAG-ASN : angle 2.22157 ( 27) hydrogen bonds : bond 0.03208 ( 373) hydrogen bonds : angle 5.17973 ( 1038) SS BOND : bond 0.00276 ( 23) SS BOND : angle 0.84578 ( 46) covalent geometry : bond 0.00351 (11786) covalent geometry : angle 0.68971 (15988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4576.33 seconds wall clock time: 87 minutes 11.17 seconds (5231.17 seconds total)